From owner-bio-software@hgmp.mrc.ac.uk  Sun Jan  2 18:08:33 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id D548617A5E; Sun,  2 Jan 2000 18:08:32 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA00897
	for <bio-software-list@hgmp.mrc.ac.uk>; Sun, 2 Jan 2000 18:08:25 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA01232
	for bio-software-list@hgmp.mrc.ac.uk; Sun, 2 Jan 2000 18:08:24 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: lisa_crawford@cmagroup.com
X-Newsgroups: bionet.software
Subject: Washington; Sr. Software Engineer; Medical Imaging, OpenGL, DirectX, graphics, PC Video,
Organization: Career Marketing Associates
Lines: 55
Message-ID: <lrMb4.1604$wv4.248937@den-news1.rmi.net>
Date: Sun, 02 Jan 2000 18:05:05 GMT
X-Complaints-To: news@rmi.net
X-Trace: den-news1.rmi.net 946836305 206.247.5.216 (Sun, 02 Jan 2000 11:05:05 MST)
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


Seattle, Washington; Sr. Software Engineer; OpenGL, DirectX, graphics, 
PC Video, multimedia

-Title: Senior Software Engineer
-Location: Seattle, WA 
-Salaried ($60-85,000), Excellent Benefits   (relocation assistance offered 
by client)  


This professional will perform the software requirements analysis, design, 
and implementation for the next generation medical imaging graphics sub-
system. The subsystem will profide services to synchronize, capture, and 
playback (multiple streams) of both uncompressed and compressed video 
and audio in realtime. 

Be familiar with multimedia solutions which are commercially available 
and with developing custom solutions. Implement and maintain requirements 
and design documentation. Devise automated and manual tests for regression 
and new feature testing. 

Requirements: 

Software development experience in C/C++ in a PC/NT environment. Should 
have experience with DirectX, OpenGL, and PC multimedia application development. 
Understanding of interrupts, DMA, queues, stacks, shared memory, and serial 
and parallel I/O design. Experience with emulators, symbolic debuggers, 
and/or simulation tools. Familiarity with test equipment: logic analyzers, 
oscilloscopes, and DVMs. Experience developing scalable software systems 
is a plus.

Strong Software Engineering Background. Thorough knowledge of embedded 
software/hardware systems, and Object Oriented design. Experience developing 
multimedia applications on Win95/98/NT. Expertise in real-time software 
design and programming in embedded systems. Good hardware/software diagnostic 
and debugging skills. Able to characterize problems quickly. Versatile, 
proactive, self-starter. Able to quickly and independently learn and apply 
new skills. Able to work from very general requirements. Enjoys and thrives 
on a wide variety of programming and organizational activities. 

Good verbal and written communication skills. A team player who will cooperate 
and collaborate with other engineers to produce an optimum solution. Demonstrates 
an understanding of the Software Life Cycle, and sound SW Engineering 
practices.

Please refer to JO# 11278RJS in your response.

lisa_crawford@cmagroup.com 

Lisa Crawford
Sr. Researcher & Associate Recruiter
ljc@cmagroup.com
IT & Software Solutions Team
Career Marketing Associates



From owner-bio-software@hgmp.mrc.ac.uk  Sun Jan  2 21:40:29 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id AA50F17A56; Sun,  2 Jan 2000 21:40:28 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA09031
	for <bio-software-list@hgmp.mrc.ac.uk>; Sun, 2 Jan 2000 21:40:27 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA11899
	for bio-software-list@hgmp.mrc.ac.uk; Sun, 2 Jan 2000 21:40:22 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: lisa_crawford@cmagroup.com
X-Newsgroups: bionet.software
Subject: Colorado; Sr. Software Engineer; NT, C++, DICOM, Imaging
Organization: Career Marketing Associates
Lines: 26
Message-ID: <2yPb4.1746$wv4.255424@den-news1.rmi.net>
Date: Sun, 02 Jan 2000 21:37:02 GMT
X-Complaints-To: news@rmi.net
X-Trace: den-news1.rmi.net 946849022 206.247.5.216 (Sun, 02 Jan 2000 14:37:02 MST)
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


Colorado; Sr. Software Engineer; NT, C++, DICOM, Imaging

**We are also working similar medical imaging software positions for clients 
in NE USA, Midwest, PNW, Texas, CA and BC Canada.  

-Senior Software Engineer
-Greater Denver/Boulder
-Salaried, Full-Time, Excellent Benefits 
(Relocation Assistance Available)

Medical DICOM knowledge important. 
Experience with C/C++ and NT required. 
Image manipulation, compression, edge detection, analysis, all good things 
to have. 

Please refer to JO# 7657RJS in your response.

lisa_crawford@cmagroup.com 

Lisa Crawford
Sr. Researcher & Associate Recruiter
ljc@cmagroup.com
IT & Software Solutions Team
Career Marketing Associates



From owner-bio-software@hgmp.mrc.ac.uk  Sun Jan  2 21:44:54 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 3FB1D17A56; Sun,  2 Jan 2000 21:44:54 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA09213
	for <bio-software-list@hgmp.mrc.ac.uk>; Sun, 2 Jan 2000 21:44:52 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA12012
	for bio-software-list@hgmp.mrc.ac.uk; Sun, 2 Jan 2000 21:44:51 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: lisa_crawford@cmagroup.com
X-Newsgroups: bionet.software
Subject: Washington; Software Engineer; Medical Imaging, NT,C++,MFC
Organization: Career Marketing Associates
Lines: 30
Message-ID: <gCPb4.1752$wv4.255511@den-news1.rmi.net>
Date: Sun, 02 Jan 2000 21:41:32 GMT
X-Complaints-To: news@rmi.net
X-Trace: den-news1.rmi.net 946849292 206.247.5.216 (Sun, 02 Jan 2000 14:41:32 MST)
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


Seattle, Washington;  Software Engineer; NT,C++,MFC
-Title:Software Engineer
-Location: Seattle, WA 
-Salaried, Good Benefits 
(relocation assistance offered by client)  

NT software engineer to work with senior image processing engineer on 
embedding 3D.

Attributes:
(1) 1+ years NT Visual C++ experience.
(2) Very important! - Self starter/proactive/energetic.
(3) Knowledge of Microsoft MFC,STL,ATL,ActiveX,DirectX,COM.
(4) OOD/OOA.
(5) Image processing experience would be a plus but would settle for someone 
who has willingness to learn.

Will consider a MSCS/MSEE right out of school if the right person.

Please refer to JO# 9749RJS in your response.

lisa_crawford@cmagroup.com 

Lisa Crawford
Sr. Researcher & Associate Recruiter
ljc@cmagroup.com
IT & Software Solutions Team
Career Marketing Associates



From owner-bio-software@hgmp.mrc.ac.uk  Mon Jan  3 14:35:35 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 0070217A43; Mon,  3 Jan 2000 14:35:34 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA24048
	for <bio-software-list@hgmp.mrc.ac.uk>; Mon, 3 Jan 2000 14:35:33 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA23920
	for bio-software-list@hgmp.mrc.ac.uk; Mon, 3 Jan 2000 14:35:32 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Josep Francesc Abril Ferrando <jabril@imim.es>
X-Newsgroups: bionet.software
Subject: GFF2PS Released...
Date: Mon, 03 Jan 2000 13:44:15 +0100
Organization: imim
Lines: 41
Message-ID: <3870999F.58B1F5AA@imim.es>
Mime-Version: 1.0
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit
Disposition-Notification-To: Josep Francesc Abril Ferrando <jabril@imim.es>
X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5-15 i686)
X-Accept-Language: ca,es,en-US
To: GFF Mailing List <gff-list@sanger.ac.uk>
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


               ------ ANNOUNCING GFF2PS ------

    gff2ps is a program for visualizing annotations of genomic sequences.
The program takes as input the annotated features on a genomic sequence
in GFF format, and produces a visual output in PostScript. It can be used
in a very simple way, because it assumes that the GFF file itself carries
enough formatting information. It also allows through a number of options
and/or a configuration file, for a great degree of customization.

    gff2ps v0.93 has been released, this version is fully operative,
handling unsorted GFF-records, multiple media sizes, and vertical pagination.
A complete user's manual explaining how to use gff2ps is included in the tar
file, which contains few examples too.

You can download it from our ftp server:

    ftp://www1.imim.es/pub/gff_tools/gff2ps/

or visit gff2ps homepage:

 http://www1.imim.es/~jabril/GFFTOOLS/GFF2PS.html

which is also available following the GFF2PS link from my home page:

 http://www1.imim.es/~jabril/

---

JOSEP FRANCESC ABRIL FERRANDO

Institut Municipal d'Investigació Mèdica
GENOME INFORMATICS GROUP
C/ Dr. Aiguader 80
08003 - Barcelona (SPAIN)
Ph:  +34 93 2211009 ext 2016
Fax: +34 93 2213237

http://www1.imim.es/~jabril




From owner-bio-software@hgmp.mrc.ac.uk  Mon Jan  3 18:39:17 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id A2F4D17A5F; Mon,  3 Jan 2000 18:39:16 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA07100
	for <bio-software-list@hgmp.mrc.ac.uk>; Mon, 3 Jan 2000 18:39:14 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA26972
	for bio-software-list@hgmp.mrc.ac.uk; Mon, 3 Jan 2000 18:39:13 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: rph@cse.ucsc.edu (Richard Hughey)
X-Newsgroups: bionet.software
Subject: SAM HMM Software Version 3.0
Date: 3 Jan 2000 18:39:08 GMT
Organization: UC Santa Cruz CIS/CE
Lines: 68
Message-ID: <84qqcc$9sh@darkstar.ucsc.edu>
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

            We are pleased to announce release of UCSC's

		  SAM Version 3.0 with SAM-T99

	 http://www.cse.ucsc.edu/research/compbio/sam.html


The Sequence Alignment and Modeling system (SAM) is a collection of
flexible software tools for creating, refining, and using linear
(profile) hidden Markov models for biological sequence analysis.  The
model states can be viewed as representing the sequence of columns in
a multiple sequence alignment, with provisions for arbitrary
position-dependent insertions and deletions in each sequence.  The
models are trained on a family of protein or nucleic acid sequences
using an expectation-maximization algorithm and a variety of
algorithmic heuristics.  A trained model can then be used to both
generate multiple alignments and search databases for new members of
the family.

For the first time, SAM includes scripts for the SAM-T99 method of
remote homology detection.  SAM-T99 is an iterative HMM search method
for creating an HMM from a single protein sequence or seed alignment
using iterative search of a protein database.  The method is currently
the most sensitive purely-sequence-based remote homology detection
algorithm [Park et al, JMB 284(4):1201-1210,1998].  SAM-T99 is based
on successful methods created for the CASP2 and CASP3 protein
structure prediction experiments [Karplus et al, Proteins,
Sup.1:134-139,1997 and Sup.3:121-125,1999].

Other additions include the use of reverse-sequence null models
[Barrett et al, Bioinformatics 14(10):846-856,1998], the calculation
of E-values, and constrained alignment and training.

SAM is available in binary distribution for unix, linux, and freebsd
platforms.

SAM is FREE for academic and non-profit use, but requires a signed
hardcopy license agreement if you do not already have one.  The
license agreement is available from the WWW site.

The license agreement, papers, documentation, and more information on
SAM can be found at:

    http://www.cse.ucsc.edu/research/compbio/sam.html


Servers for performing SAM-T98 structure prediction (SAM-T99 to
available soon) using our library of HMMs is available at:

   http://www.cse.ucsc.edu/research/compbio/HMM-apps/HMM-applications.html


The server will soon be accelerated with the UCSC Kestrel parallel processor: 

   http://www.cse.ucsc.edu/research/kestrel




Kevin Karplus
Mark Diekhans
Richard Hughey

saminfo@cse.ucsc.edu

Department of Computer Engineering
University of California
Santa Cruz, CA 95064


From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan  4 10:25:06 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 4037B17A62; Tue,  4 Jan 2000 10:25:06 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA05279
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 4 Jan 2000 10:25:04 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA16631
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 4 Jan 2000 10:25:02 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Simon Dray" <simon.dray@bbsrc.ac.uk>
X-Newsgroups: bionet.software
Subject: test
Date: Tue, 4 Jan 2000 10:10:17 -0000
Organization: BBSRC Biotechnology and Biological Sciences Research Council
Lines: 3
Message-ID: <84sgqr$nrb$1@news.bbsrc.ac.uk>
X-Newsreader: Microsoft Outlook Express 4.72.3110.5
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

test message please ignore




From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan  4 10:38:18 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 45FAA17A62; Tue,  4 Jan 2000 10:38:18 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA07143
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 4 Jan 2000 10:38:16 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA16751
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 4 Jan 2000 10:38:15 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: olam@radium.uio.no (Ola Myklebost)
X-Newsgroups: bionet.software
Subject: Post doc position in Norway: Data Mining/Bioinformatics
Date: Tue, 04 Jan 2000 11:38:12 +0100
Organization: Norwegian Radium Hospital
Lines: 23
Message-ID: <olam-0401001138130001@pcdnr05.uio.no>
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


A three year post doc position is available at the Microarray Centre
at the Institute for Cancer research / Norwegian Radium Hospital in
Oslo, Norway.

We are preferably looking for a computer scientist or
bioinformatician, but are also interested in molecular biologists
with some competence in bioinformatics or computer science.
Experience with microarrays will be an advantage.

Please look at http://www.med.uio.no/dnr/microarray/postdoc.html


Ola Myklebost, Professor, Dr Philos       University of Oslo

Dept of Tumor Biology             Tel (Office):   +47-2293-4299 (-5936)
Institute for Cancer Research     Switchboard:    +47-2293-4000
The Norwegian Radium Hospital     Fax:            +47-2252-2421
Montebello                        Pager:          +47-9681-8125
N-0310 OSLO, Norway               Email (org): ola.myklebost@labmed.uio.no
                                  or (machine address): olam@radium.uio.no

WWW presentation: http://www.med.uio.no/dnr/People/Ola.html


From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan  4 13:50:11 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 889DB17A63; Tue,  4 Jan 2000 13:50:10 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA24536
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 4 Jan 2000 13:50:08 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA19146
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 4 Jan 2000 13:50:07 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Harold Drabkin" <hdrabkin@user1.channel1.com>
X-Newsgroups: bionet.software
Subject: excel add-in
Date: Tue, 4 Jan 2000 08:46:39 -0500
Organization: Posted via Supernews, http://www.supernews.com
Lines: 5
Message-ID: <s73uj26s5k249@corp.supernews.com>
X-Complaints-To: newsabuse@supernews.com
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2615.200
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Some time ago, I saw an add-in or program that essentially aided using excel
for scientific charting, etc.; some sort of collection of macros, templates,
etc. I'm now using excel 2000.  Does anyone have a lead on such a thing?




From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan  4 15:22:39 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id DAF2617A63; Tue,  4 Jan 2000 15:22:38 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA07616
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 4 Jan 2000 15:22:37 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA20418
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 4 Jan 2000 15:22:36 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Claude Jakob" <Jakob@micro.biol.ethz.ch>
X-Newsgroups: bionet.software
Subject: Looking for Cloning Software
Date: Tue, 4 Jan 2000 16:25:12 +0100
Lines: 77
MIME-Version: 1.0
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_002B_01BF56D0.46BD9880"
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2919.6600
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600
Message-ID: <38721032.0@pfaff.ethz.ch>
X-Trace: 4 Jan 2000 16:22:26 +0100, d42-gx1p.ethz.ch
Organization: Swiss Federal Institute of Technology (ETHZ)
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

This is a multi-part message in MIME format.

------=_NextPart_000_002B_01BF56D0.46BD9880
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Hi,

I am currently looking for (evaluating) DNA cloning software (e.g. for =
manipulation of plasmids and fragments with correct terminior in silica =
cloning , such as Clone Manager) for our PC platform. Apart from "Clone =
Manager" I did not find very much in the field.=20

If anybody could provide me with information of other cloning programs =
(Windows 95/98/NT) I would be very grateful.

Thanks,Claude

-----------------------------------------------------------------------
Claude A. Jakob, Ph.D.
Institute for Microbiology, ETH Zuerich
Schmelzbergstrasse 7
CH-8092 Zuerich
Switzerland
=20
Phone: +41-1-632-3327
Fax:      +41-1-632-1148
email:  jakob@micro.biol.ethz.ch
www:   http://www.micro.biol.ethz.ch/~jakobc

------=_NextPart_000_002B_01BF56D0.46BD9880
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content=3D"text/html; charset=3Diso-8859-1" =
http-equiv=3DContent-Type>
<META content=3D"MSHTML 5.00.2919.6307" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY>
<DIV><FONT size=3D2>Hi,</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>I am currently looking for (evaluating) DNA cloning =
software=20
(e.g. for manipulation of plasmids and fragments with correct terminior =
<EM>in=20
silica </EM>cloning , such as Clone Manager) for&nbsp;our PC platform. =
Apart=20
from "Clone Manager" I did not find very much in the field. =
</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>If anybody could provide me with information of =
other cloning=20
programs (Windows 95/98/NT) I would be very grateful.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>Thanks,</FONT><FONT size=3D2>Claude</FONT></DIV>
<DIV><BR><FONT=20
size=3D2>----------------------------------------------------------------=
-------<BR>Claude=20
A. Jakob, Ph.D.<BR>Institute for Microbiology, ETH =
Zuerich<BR>Schmelzbergstrasse=20
7<BR>CH-8092 Zuerich<BR>Switzerland<BR>&nbsp;<BR>Phone:=20
+41-1-632-3327<BR>Fax:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
+41-1-632-1148<BR>email:&nbsp; </FONT><A=20
href=3D"mailto:jakob@micro.biol.ethz.ch"><FONT=20
size=3D2>jakob@micro.biol.ethz.ch</FONT></A><BR><FONT =
size=3D2>www:&nbsp;&nbsp;=20
</FONT><A href=3D"http://www.micro.biol.ethz.ch/~jakobc"><FONT=20
size=3D2>http://www.micro.biol.ethz.ch/~jakobc</FONT></A></DIV></BODY></H=
TML>

------=_NextPart_000_002B_01BF56D0.46BD9880--



From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan  4 16:01:14 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 5927917A5A; Tue,  4 Jan 2000 16:01:14 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA11352
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 4 Jan 2000 16:01:12 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA20812
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 4 Jan 2000 16:01:11 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Przemko Tylzanowski <przemko@med.kuleuven.ac.be>
X-Newsgroups: bionet.software
Subject: Merging bright fiels and fluorescence
Date: Tue, 04 Jan 2000 17:08:37 +0100
Organization: KULeuvenNet
Lines: 21
Message-ID: <38721B05.322AFAE6@med.kuleuven.ac.be>
Mime-Version: 1.0
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: naxos.belnet.be 947001647 10289 134.58.127.3 (4 Jan 2000 16:00:47 GMT)
X-Complaints-To: abuse@belnet.be
X-Mailer: Mozilla 4.7 [en] (WinNT; I)
X-Accept-Language: en
Cache-Post-Path: marvin!unknown@joint.med.kuleuven.ac.be
X-Cache: nntpcache 2.3.3 (see http://www.nntpcache.org/)
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
Hi!
<br>We have a SPOT camera system and a software that comes with it. Unfortunately
the software (as good as it is) cannot merge bright field and fluorescence
images (for instance Nomarski with CY2).
<br>Is anyone of you aware of a software that could do that?
<br>TIA
<br>Przemko
<p>--
<br>Przemko Tylzanowski Ph.D.
<br>LSD &amp; Joint
<br>O &amp; N
<br>University of Leuven
<br>Herestraat 49
<br>3000 Leuven
<br>Belgium
<p>phone: (32-16)34-61-96
<br>fax&nbsp; : (32-16)34-62-00
<br>&nbsp;</html>



From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan  4 16:05:15 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id CF6CC17A5A; Tue,  4 Jan 2000 16:05:14 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA11708
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 4 Jan 2000 16:05:13 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA20949
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 4 Jan 2000 16:05:12 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Soeren W. Rasmussen" <swr@crc.dk>
X-Newsgroups: bionet.software
Subject: Re: Looking for Cloning Software
Date: Tue, 04 Jan 2000 16:59:25 +0100
Organization: UNI-C
Lines: 88
Message-ID: <387218DD.869BCBB6@crc.dk>
References: <38721032.0@pfaff.ethz.ch>
Mime-Version: 1.0
Content-Type: multipart/alternative;
 boundary="------------E858269DC9B68F5F21AA0FE6"
X-Trace: news.net.uni-c.dk 947001721 54258 130.226.182.97 (4 Jan 2000 16:02:01 GMT)
X-Complaints-To: usenet@news.net.uni-c.dk
X-Mailer: Mozilla 4.7 [en] (Win95; I)
X-Accept-Language: en
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


--------------E858269DC9B68F5F21AA0FE6
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

DNATools has some fairly simple options for building plasmids on the
basis of restriction enzyme digests. If you wish to try it, a fully
functional, free demo copy can be downloaded from our homepage .

Regards

Soeren

Claude Jakob wrote:

> Hi, I am currently looking for (evaluating) DNA cloning software (e.g.
> for manipulation of plasmids and fragments with correct terminior in
> silica cloning , such as Clone Manager) for our PC platform. Apart
> from "Clone Manager" I did not find very much in the field. If anybody
> could provide me with information of other cloning programs (Windows
> 95/98/NT) I would be very grateful. Thanks,Claude
>
> ----------------------------------------------------------------------
>
> Claude A. Jakob, Ph.D.
> Institute for Microbiology, ETH Zuerich
> Schmelzbergstrasse 7
> CH-8092 Zuerich
> Switzerland
>
> Phone: +41-1-632-3327
> Fax:      +41-1-632-1148
> email:  jakob@micro.biol.ethz.ch
> www:   http://www.micro.biol.ethz.ch/~jakobc

--
Dr. scient. Søren W. Rasmussen
Carlsberg Laboratory, Department of Physiology
10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark
Phone  45 33275230/45 36162259, Fax 45 33274766
swr@crc.dk, http://www.crc.dk/phys/

DNATools sequencing software:
http://www.crc.dk/phys/dnatools.htm


--------------E858269DC9B68F5F21AA0FE6
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
DNATools has some fairly simple options for building plasmids on the basis
of restriction enzyme digests. If you wish to try it, a fully functional,
free demo copy can be downloaded from our homepage .
<p>Regards
<p>Soeren
<p>Claude Jakob wrote:
<blockquote TYPE=CITE><style></style>
<font size=-1>Hi,</font> <font size=-1>I
am currently looking for (evaluating) DNA cloning software (e.g. for manipulation
of plasmids and fragments with correct terminior <i>in silica </i>cloning
, such as Clone Manager) for our PC platform. Apart from "Clone Manager"
I did not find very much in the field.</font> <font size=-1>If anybody
could provide me with information of other cloning programs (Windows 95/98/NT)
I would be very grateful.</font> <font size=-1>Thanks,Claude</font>
<br><font size=-1>-----------------------------------------------------------------------</font>
<br><font size=-1>Claude A. Jakob, Ph.D.</font>
<br><font size=-1>Institute for Microbiology, ETH Zuerich</font>
<br><font size=-1>Schmelzbergstrasse 7</font>
<br><font size=-1>CH-8092 Zuerich</font>
<br><font size=-1>Switzerland</font>
<p><font size=-1>Phone: +41-1-632-3327</font>
<br><font size=-1>Fax:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; +41-1-632-1148</font>
<br><font size=-1>email:&nbsp; <a href="mailto:jakob@micro.biol.ethz.ch">jakob@micro.biol.ethz.ch</a></font>
<br><font size=-1>www:&nbsp;&nbsp; <a href="http://www.micro.biol.ethz.ch/~jakobc">http://www.micro.biol.ethz.ch/~jakobc</a></font></blockquote>
--
<br>Dr. scient. S&oslash;ren W. Rasmussen
<br>Carlsberg Laboratory, Department of Physiology
<br>10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark
<br>Phone&nbsp; 45 33275230/45 36162259, Fax 45 33274766
<br>swr@crc.dk, <A HREF="http://www.crc.dk/phys/">http://www.crc.dk/phys/</A>
<p>DNATools sequencing software:
<br><A HREF="http://www.crc.dk/phys/dnatools.htm">http://www.crc.dk/phys/dnatools.htm</A>
<br>&nbsp;</html>

--------------E858269DC9B68F5F21AA0FE6--



From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan  4 19:26:26 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id E484217AE7; Tue,  4 Jan 2000 19:26:25 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA03250
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 4 Jan 2000 19:26:24 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA24337
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 4 Jan 2000 19:26:22 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Andrew Rambaut <andrew.rambaut@zoo.ox.ac.uk>
X-Newsgroups: bionet.software
Subject: New tree manipulation program.
Date: Tue, 04 Jan 2000 17:58:51 +0000
Organization: Oxford University, England
Lines: 49
Message-ID: <040120001758515661%andrew.rambaut@zoo.ox.ac.uk>
Mime-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 8bit
X-Trace: news.ox.ac.uk 947008732 28330 163.1.210.37 (4 Jan 2000 17:58:52 GMT)
X-Complaints-To: newsmaster@ox.ac.uk
User-Agent: YA-NewsWatcher/4.2.6
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


I would like to announce the first, highly preliminary, alpha version
of my new tree manipulation package. TreeEdit is an application for
organising, viewing and manipulating sets of phylogenetic trees. It is
intended as a tool for preparing sets of trees for use in phylogenetics
packages such as PAUP. 

Runs on Macintosh (PowerMacs) under MacOS 8.5 or above (actually
only tested on 8.5 and above may work on previous systems).

<http://evolve.zoo.ox.ac.uk/TreeEdit/TreeEdit.html>

Features

*  The import and export of trees in a range of commonly used formats.
These include PHYLIP (NEWICK), NEXUS (PAUP and MacClade) and CAIC
formats. 
*  Full drag-and-drop of trees between windows, to the desktop as a
"clipping" or to text editors. In the case of the latter two options,
the trees are written as a NEXUS file. 
*  Cut and Pasting of trees between TreeEdit and text editors (again
the trees are written as a NEXUS file). They can be pasted directly
into PAUP. 
*  Root the tree by clicking on the branch (or node) on which you wish
the root to lie. Midpoint rooting is also available. 
*  Include and exclude taxa or clades. Excluded branches are drawn as
"greyed-out" or can be hidden altogether. Trees can be written without
the excluded taxa. 
*  Edit taxon labels. 
*  Rotate branch order at a node. 
*  Drag and drop editing of branches. 
*  Collapse branches to produce polytomies. 
*  Randomly resolve polytomies. 
*  A set of trees can be "linked" so that an operation done on one is
performed on all the others (if possible). This option is limited to a
few operations at present. 


------------------------------------------------------------------------

The following features are still to be implemented:


*  Er.. lots - please feel free to suggest some more. 
*  The name might even be improved.

------------------------------------------------------------------------

Andrew


From owner-bio-software@hgmp.mrc.ac.uk  Wed Jan  5 21:35:02 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 5871717A5B; Wed,  5 Jan 2000 21:35:02 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA09902
	for <bio-software-list@hgmp.mrc.ac.uk>; Wed, 5 Jan 2000 21:35:00 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA00136
	for bio-software-list@hgmp.mrc.ac.uk; Wed, 5 Jan 2000 21:34:59 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Roland Hubner <rhubner@hgins.uia.ac.be>
X-Newsgroups: bionet.software
Subject: Re: Merging bright fiels and fluorescence
Date: Wed, 05 Jan 2000 22:34:52 +0100
Organization: Lab. of Pathology, University of Antwerpen
Lines: 11
Message-ID: <rhubner-6D8591.22345205012000@news.uia.ac.be>
References: <38721B05.322AFAE6@med.kuleuven.ac.be>
Mime-Version: 1.0
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit
X-Trace: naxos.belnet.be 947108094 6342 143.169.254.1 (5 Jan 2000 21:34:54 GMT)
X-Complaints-To: abuse@belnet.be
User-Agent: MT-NewsWatcher/3.0 (PPC)
X-Original-NNTP-Posting-Host: macgens10.uia.ac.be
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Happy New Year Przemko!

> cannot merge bright field and fluorescence images (for instance Nomarski
> with CY2).
...
> LSD; Joint

 I would rather suggest contacting www.biotech.missouri.edu/mcc/mccf.html

Have fun,
 Roland


From owner-bio-software@hgmp.mrc.ac.uk  Thu Jan  6 07:50:18 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id B978117A56; Thu,  6 Jan 2000 07:50:17 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id HAA23001
	for <bio-software-list@hgmp.mrc.ac.uk>; Thu, 6 Jan 2000 07:50:16 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA07528
	for bio-software-list@hgmp.mrc.ac.uk; Thu, 6 Jan 2000 07:50:14 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: mhabio@my-deja.com
X-Newsgroups: bionet.software
Subject: ANN: Fermentor Control Software version 2.0
Date: Thu, 06 Jan 2000 07:40:10 GMT
Organization: Deja.com - Before you buy.
Lines: 26
Message-ID: <851gsp$ak9$1@nnrp1.deja.com>
X-Article-Creation-Date: Thu Jan 06 07:40:10 2000 GMT
X-Http-User-Agent: Mozilla/4.7 [en] (Win95; I)
X-Http-Proxy: 1.0 x34.deja.com:80 (Squid/1.1.22) for client 130.225.8.202
X-MyDeja-Info: XMYDJUIDmhabio
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Version 2.0 of the Control Software for the BioStat Fermentors has been
released. (Freeware)

Version 2.0 has several new features like Timed Events and Profiles,
Fuzzy Logic Substrate Control, and Internet Client is available. Program
works with Biostat A, B, C, D, Micro-DCU, & DCU.

The BioStat control program collects process data and display them in a
graphical window. All process set points are controlled by graphical
sliders or by keyboard, and numerical displays show the current
settings. Intelligent control to master substrate addition is possible
with the fuzzy logic control module. Timed events/profiles can be
designed with the profile editor. Finally, a TCP/IP client makes it
possible to control the unit from any online computer in the world.

Please find more information and screen shots on the BioStat Control
Software homepage: http://imsb.au.dk/~mha/biohome.htm

--
Regards,
Mikkel H. Andersen



Sent via Deja.com http://www.deja.com/
Before you buy.


From owner-bio-software@hgmp.mrc.ac.uk  Thu Jan  6 14:00:15 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 8769317B23; Thu,  6 Jan 2000 14:00:14 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA23264
	for <bio-software-list@hgmp.mrc.ac.uk>; Thu, 6 Jan 2000 14:00:11 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA12938
	for bio-software-list@hgmp.mrc.ac.uk; Thu, 6 Jan 2000 14:00:10 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: gbottu@bigben.vub.ac.be (Guy Bottu)
X-Newsgroups: bionet.software
Subject: where can I get recent elm/mm ?
Date: 6 Jan 2000 13:53:19 GMT
Organization: Brussels Free Universities VUB/ULB
Lines: 12
Message-ID: <8526of$4dr$1@mach.vub.ac.be>
X-Newsreader: TIN [version 1.2 PL2]
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

I have a question. Where can I find the most recent version of the mail
client elm ? Version 2.4.25 is not Y2K compliant. It sends messages with
the year 100 in the date. I have seen that there exists a version 2.5
that does not have this bug. However, at the anonymous ftp site
nic.funet.fi the last available version is 2.4.25.

Is there also a version of mm (MetaMail) beyond 2.7 ? Version 2.7 does
not compile under Solaris.

	Thank you in advance,
	  Guy Bottu,
	Belgian EMBnet Node


From owner-bio-software@hgmp.mrc.ac.uk  Thu Jan  6 15:29:19 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 91DD817A83; Thu,  6 Jan 2000 15:29:18 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA01353
	for <bio-software-list@hgmp.mrc.ac.uk>; Thu, 6 Jan 2000 15:29:16 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA14088
	for bio-software-list@hgmp.mrc.ac.uk; Thu, 6 Jan 2000 15:29:15 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: jkb@mrc-lmb.cam.ac.uk (James Bonfield)
X-Newsgroups: bionet.software
Subject: Re: where can I get recent elm/mm ?
Date: 6 Jan 2000 15:29:14 GMT
Organization: MRC Laboratory of Molecular Biology, Cambridge UK
Lines: 27
Message-ID: <852cca$9j8$1@pegasus.csx.cam.ac.uk>
References: <8526of$4dr$1@mach.vub.ac.be>
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

In article <8526of$4dr$1@mach.vub.ac.be> gbottu@bigben.vub.ac.be (Guy Bottu) writes:
>I have a question. Where can I find the most recent version of the mail
>client elm ? Version 2.4.25 is not Y2K compliant. It sends messages with
>the year 100 in the date. I have seen that there exists a version 2.5
>that does not have this bug. However, at the anonymous ftp site
>nic.funet.fi the last available version is 2.4.25.

Try http://ftpsearch.lycos.com/?form=medium for a good ftp search engine.

Look for elm-2.4ME+66.tar.gz or elm2.5.2.
I prefer 2.4ME (a spin-off of 2.4) as it has better handling of MIME than
2.5.2. Also see the elm newsgroup (I forget what it's called) for a Y2K patch
to 2.5.2, as even that still has some problems.

I used elm until a few days ago, and found the same problem. The
authors of 2.4ME appear to have got fed up with the problems in elm
and so wrote their own from scratch, called Mutt. I'm now using this
and I find it far superior, and very easy to use if you are used to
the elm keybindings. I cannot remember the mutt home page, but I'm
sure a few altavista searches will pick it out.

	James
--
James Bonfield (jkb@mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/


From owner-bio-software@hgmp.mrc.ac.uk  Thu Jan  6 15:52:10 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id D19E817A7B; Thu,  6 Jan 2000 15:52:09 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA04550
	for <bio-software-list@hgmp.mrc.ac.uk>; Thu, 6 Jan 2000 15:52:05 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA14490
	for bio-software-list@hgmp.mrc.ac.uk; Thu, 6 Jan 2000 15:52:04 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Tim Cutts <timc@chiark.greenend.org.uk>
X-Newsgroups: bionet.software
Subject: Re: where can I get recent elm/mm ?
Date: 06 Jan 2000 15:50:10 +0000 (GMT)
Organization: Linux Unlimited
Lines: 14
Message-ID: <2qc*S5sho@news.chiark.greenend.org.uk>
References: <8526of$4dr$1@mach.vub.ac.be> <852cca$9j8$1@pegasus.csx.cam.ac.uk>
X-Newsreader: trn 4.0-test70 (17 January 1999)
Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1])
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

In article <852cca$9j8$1@pegasus.csx.cam.ac.uk>,
James Bonfield <jkb@mrc-lmb.cam.ac.uk> wrote:
>authors of 2.4ME appear to have got fed up with the problems in elm
>and so wrote their own from scratch, called Mutt. I'm now using this
>and I find it far superior, and very easy to use if you are used to
>the elm keybindings. I cannot remember the mutt home page, but I'm
>sure a few altavista searches will pick it out.

I use mutt as well.  It is absolutely superb.

http://www.mutt.org

Tim.



From owner-bio-software@hgmp.mrc.ac.uk  Thu Jan  6 18:16:47 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 41AFA17B2B; Thu,  6 Jan 2000 18:16:47 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA19920
	for <bio-software-list@hgmp.mrc.ac.uk>; Thu, 6 Jan 2000 18:16:45 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA16407
	for bio-software-list@hgmp.mrc.ac.uk; Thu, 6 Jan 2000 18:16:44 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Piotr Kozbial <piotrk@ibb.waw.pl>
X-Newsgroups: bionet.software
Subject: Re: where can I get recent elm/mm ?
Date: Thu, 06 Jan 2000 19:17:29 +0100
Organization: http://news.icm.edu.pl/
Lines: 16
Message-ID: <3874DC39.2277DF7B@ibb.waw.pl>
References: <8526of$4dr$1@mach.vub.ac.be>
Reply-To: piotrk-NO@SPAMM-ibb.waw.pl
Mime-Version: 1.0
Content-Type: text/plain; charset=iso-8859-2
Content-Transfer-Encoding: 7bit
X-Trace: sunsite.icm.edu.pl 947182600 15605 212.87.28.79 (6 Jan 2000 18:16:40 GMT)
X-Complaints-To: abuse@news.icm.edu.pl
X-Accept-Language:  en
X-Mailer:  Mozilla 4.7 [en] (X11; U; Linux 2.2.10 i686)
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Guy Bottu wrote:
> 
> I have a question. Where can I find the most recent version of the mail
> client elm ? Version 2.4.25 is not Y2K compliant. It sends messages with
> the year 100 in the date. I have seen that there exists a version 2.5
> that does not have this bug. However, at the anonymous ftp site
> nic.funet.fi the last available version is 2.4.25.
> 
> Is there also a version of mm (MetaMail) beyond 2.7 ? Version 2.7 does
> not compile under Solaris.
> 
>         Thank you in advance,
>           Guy Bottu,
>         Belgian EMBnet Node

http://www.uwsg.indiana.edu/y2k/elmy2k.html


From owner-bio-software@hgmp.mrc.ac.uk  Thu Jan  6 19:00:13 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 1D36E17A75; Thu,  6 Jan 2000 19:00:12 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA23236
	for <bio-software-list@hgmp.mrc.ac.uk>; Thu, 6 Jan 2000 19:00:11 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA16887
	for bio-software-list@hgmp.mrc.ac.uk; Thu, 6 Jan 2000 19:00:10 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Cornelius Krasel <krasel@wpxx02.toxi.uni-wuerzburg.de>
X-Newsgroups: bionet.software
Subject: Re: where can I get recent elm/mm ?
Date: Thu, 6 Jan 2000 19:07:55 +0100
Organization: =?ISO-8859-1?Q?Universit=E4t_W=FCrzburg?=
Lines: 19
Message-ID: <rll258.do7.ln@wpxx02.toxi.uni-wuerzburg.de>
References: <8526of$4dr$1@mach.vub.ac.be> <852cca$9j8$1@pegasus.csx.cam.ac.uk>
X-Trace: fu-berlin.de 947185202 1286384 132.187.168.2 (16 [16673])
User-Agent: tin/pre-1.4-19990805 ("Preacher Man") (UNIX) (Linux/2.2.13 (i686))
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

James Bonfield <jkb@mrc-lmb.cam.ac.uk> wrote:
> I used elm until a few days ago, and found the same problem. The
> authors of 2.4ME appear to have got fed up with the problems in elm
> and so wrote their own from scratch, called Mutt.

I think elm-2.4ME is still being maintained. I did not experience any
problems with elm-2.4ME62 Y2K- or otherwise. I prefer elm over mutt
because I don't like the design (I guess it's just me...). I agree
with James on elm-2.5.2 :-)

Mutt is available from http://www.mutt.org/ . For some reason the
server is currently very slow.

--Cornelius.

-- 
/* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */
/* D-97078 Wuerzburg, Germany   email: phak004@rzbox.uni-wuerzburg.de  SP4 */
/* "Science is the game we play with God to find out what His rules are."  */


From owner-bio-software@hgmp.mrc.ac.uk  Fri Jan  7 13:11:17 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id D956A17A69; Fri,  7 Jan 2000 13:11:15 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA15210
	for <bio-software-list@hgmp.mrc.ac.uk>; Fri, 7 Jan 2000 13:11:10 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA08413
	for bio-software-list@hgmp.mrc.ac.uk; Fri, 7 Jan 2000 13:11:09 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Tim Corp." <station@nursat.kz>
X-Newsgroups: bionet.software
Subject: Pro AVP anti-virus packet for Win95/98/NT
Date: Fri, 7 Jan 2000 18:41:01 +0600
Organization: Tim Corp.
Lines: 65
Message-ID: <854oh9$q66$1@mail.nursat.net>
X-Trace: mail.nursat.net 947250537 26822 195.82.27.80 (7 Jan 2000 13:08:57 GMT)
X-Complaints-To: usenet@news.nursat.kz
X-Newsreader: Microsoft Outlook Express 4.72.3110.5
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

John Dvorak of PC Magazine Online recommends AntiViral Toolkit Pro!
www.zdnet.com/pcmag/insites/dvorak/jd990614.htm

The next version of a professional anti-virus packet AntiViral Toolkit Pro
by Eugene Kaspersky for Windows 95, Windows 98 and Windows NT is offered to
you.

  This program - new step in struggle with computer viruses. She is
completely 32 bit applications optimized for operation in operational
Windows95 environments /98 and Windows NT and operating /98 and all
possibilities they give.

  The program has convenient user interface, characteristic of a Windows
95 environment /98, plenty of tunings sampled by the user, and also one of
largest in the world of anti-virus bases.

During operation AVP scans:
  - RAM.
  - Files, including archive and packed.
  - System sectors containing Master Boot Record, boot sector
(Boot-sector) and table of splitting of the disk (Partition Table).

The fundamental features AVP:
  - Detection and deleting of huge number of the diversified viruses,
including:
   * of the polymorphic or self-ciphered viruses;
   * of stels-viruses or virus - invisible;
   * of new viruses for Windows 3. XX and Windows 95/98;
   * macro of viruses infecting documents Word and the table Excel.

  - Scanning inside the packed files (module Unpacking Engine).
  - Scanning inside archive files (module Extracting Engine).
  - Scanning of objects on floppy, local, network and CD-ROM disks.
  - Supervision behind file operations in a system in a background and
detection of a virus up to the moment of real infection of a system with the
help of the RESIDENT SCREEN MONITOR.

  - Heuristic module Code Analyzer, necessary for detection of UNKNOWN
viruses.
  - Search in a mode of excessive scanning.
  - Convenient user interface.
  - Creation, saving and load of a plenty of various tunings.
  - Mechanism of a continuity check of an anti-virus system.
  - Power system of the help.
...................................
Tim Corp. designs, consults, develops, distributes, and markets antivirus
software, and is one of the leading antivirus companies in the Russia and
Central Asia region. Its flagship product is AntiViral Toolkit Pro.
AntiViral Toolkit Pro is developed by Kaspersky Lab, Russia www.avp.ru .
AntiViral Toolkit Pro is the copyrighted work of Kaspersky Lab, Russia.

Best price, best quality, just now price for all products AVP - 49 USD.
....................................
For More Information
....................................
Andrey Otrubennikov
Sales Director
Tim Corp.
Kazakstan 480000
Almaty P.O.Box 246
Phone: 7-3272/900-314
FAX: 7-3272/900-315
E-mail: station@nursat.kz




From owner-bio-software@hgmp.mrc.ac.uk  Fri Jan  7 19:10:09 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 5F4DF17AAA; Fri,  7 Jan 2000 19:10:08 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA21779
	for <bio-software-list@hgmp.mrc.ac.uk>; Fri, 7 Jan 2000 19:10:06 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA13037
	for bio-software-list@hgmp.mrc.ac.uk; Fri, 7 Jan 2000 19:10:05 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
X-Newsgroups: bionet.software
Subject: Re: where can I get recent elm/mm ?
Date: 7 Jan 2000 18:53:18 GMT
Organization: University of Washington Genetics
Lines: 17
Message-ID: <855cmu$13jg$1@nntp4.u.washington.edu>
References: <8526of$4dr$1@mach.vub.ac.be>
X-Trace: nntp4.u.washington.edu 947271198 36464 (None) 140.142.17.37
X-Complaints-To: help@cac.washington.edu
Summary: Where you can get elm 2.5
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

In article <8526of$4dr$1@mach.vub.ac.be>,
Guy Bottu <gbottu@bigben.vub.ac.be> wrote:
>I have a question. Where can I find the most recent version of the mail
>client elm ? Version 2.4.25 is not Y2K compliant. It sends messages with
>the year 100 in the date. I have seen that there exists a version 2.5
>that does not have this bug. However, at the anonymous ftp site
>nic.funet.fi the last available version is 2.4.25.

We had that problem too.  I found elm 2.5.2 at

    ftp://ftp.virginia.edu/pub/elm/

This solved the Y2K problem.  Note that a RedHat package for it is there too.

-- 
Joe Felsenstein         joe@genetics.washington.edu
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA


From owner-bio-software@hgmp.mrc.ac.uk  Fri Jan  7 22:31:36 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 6FCA517AD1; Fri,  7 Jan 2000 22:31:35 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA12205
	for <bio-software-list@hgmp.mrc.ac.uk>; Fri, 7 Jan 2000 22:31:33 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA23588
	for bio-software-list@hgmp.mrc.ac.uk; Fri, 7 Jan 2000 22:31:32 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: rgarcia@is05.fas.harvard.edu (Rachel M. Kadel-Garcia)
X-Newsgroups: bionet.software
Subject: phrap quality scores
Date: 7 Jan 2000 22:15:32 GMT
Organization: Harvard University, Cambridge, Massachusetts
Lines: 7
Message-ID: <slrn87cpdp.8ga.rgarcia@is05.fas.harvard.edu>
User-Agent: slrn/0.9.5.7 (UNIX)
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Does anyone here have an understanding of phrap quality scores
beyond what's in the docs?  I'm trying to figure out how to 
assign similar quality scores to assemblies not done with phrap,
and I'm resorting to spelunking in the source, but it's rough 
going.

						Rachel


From owner-bio-software@hgmp.mrc.ac.uk  Fri Jan  7 22:55:47 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id D5DF717A63; Fri,  7 Jan 2000 22:55:46 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA13820
	for <bio-software-list@hgmp.mrc.ac.uk>; Fri, 7 Jan 2000 22:55:45 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA23825
	for bio-software-list@hgmp.mrc.ac.uk; Fri, 7 Jan 2000 22:55:43 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: solovyev@sanger.ac.uk (Victor Solovyev)
X-Newsgroups: bionet.software
Subject: SUPER_LINK_Chromosome 22 Gene Predictions by FGENESH
Date: 7 Jan 2000 22:55:42 -0000
Organization: MRC Human Genome Mapping Project Resource Centre
Lines: 70
Message-ID: <200001072255.WAA08546@wallaby.sanger.ac.uk>
X-Trace: niobium.hgmp.mrc.ac.uk 947285742 23822 193.62.192.80 (7 Jan 2000 22:55:42 GMT)
X-Complaints-To: news@hgmp.mrc.ac.uk
X-Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA13813
	for <bio-software@net.bio.net>; Fri, 7 Jan 2000 22:55:41 GMT
X-Received: from wallaby.sanger.ac.uk (solovyev@wallaby [193.62.207.143])
	by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id WAA19207;
	Fri, 7 Jan 2000 22:55:29 GMT
X-Received: (from solovyev@localhost)
	by wallaby.sanger.ac.uk (8.8.7/8.8.7) id WAA08546;
	Fri, 7 Jan 2000 22:55:29 GMT
X-To: bio-software@hgmp.mrc.ac.uk
X-Cc: solovyev@bcm.tmc.edu
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

 Gene Predictions for SUPER_LINK_Chromosome 22 are available at:
             http://genomic.sanger.ac.uk/inf/infodb.shtml
             
            under CGG genomics WEB server:  http://genomic.sanger.ac.uk/    

       
 the predictions by Fgenesh program (Salamov,Solovyev,1999) 
 
 You can ftp data for your further analysis! 
                 
   Chromosome 22 predicted genes and similarity data in INFOGENE format 
   Chromosome 22 predicted proteins in fasta format 
   Chromosome 22 predicted exon sequences in fasta format 
   Chromosome 22 predicted exon amino acid sequences in fasta format 
    
Due to high accuracy exon prediction and significantly less accurate assigning 
exons to a particular gene, exon sequences itself present value to experimental 
gene verification or Other projects 
               
  Visual representation of Predicted genes as well as ALL KNOWN GENES could be 
seen in gene centred database INFOGENE through Java viewer.
    This database includes genes constructed often from many GenBank entries, 
release 114.
	
Divisions with separate collections for model organisms include:

Human genes data
Other Primates genes data
Mus musculus genes data
Other Rodenta genes data
Other Mammalia genes data       
Danio rerio genes data          
Fugu rubripes genes data
Other Vertebrata genes data
Drosophila melanogaster genes data
Caenorhabditis elegans genes data
Other Invertebrata genes data
Saccharomyces cerevisiae genes data 
Schizosaccharomyces pombe genes data
Arabidopsis thaliana genes data
Oriza Sativa genes data				* New
Zea Mays genes data				* New
Other eukaryotes from GB *.pln genes data
Annotation of Drosophila Melanogaster 2.9 MB ADH region
SUPER_LINK Chromosome 22 gene predictions        * New

Included Drosophila melanogaster ADH 2.9 MB genomic region automatic annotation
using FGENES and FGENESH: Fgenes predictions, Fgenesh predictions, CGG1 -
summary prediction using both mention above and std3 - manual annotation based o
nexperimental data (some computational) by Ashburner et al. (1999).
  This example shows problems with genomic annotation: 90% of actual coding
sequences predicted accurately, but exons often combined very different
from real genes.

- You can save an Infogene record using Action menu and Obtain Infogene
locus option (with or without sequence)
- Realized search of context (select Search filds (among many specific
  lines of Infogen database) and print your word in left down corner)
  For example you can find all genes which have start of transcription
  annotated in GeneBank: Select Context in Option menu,
  select onlt TSP field in SearchFilds, put * in search window and Enter.

To see all information about a gene in the locus:
    Put mouse pointer to gene block
   in upper window and push and keep right mouse button
   (shift key + push and click right mouse button will permanently
    show this information)
LocusInfo button will show a head of locus which shows how many GenBank
entries are used for gene description
---


From owner-bio-software@hgmp.mrc.ac.uk  Sat Jan  8 02:10:11 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 724D017ADE; Sat,  8 Jan 2000 02:10:10 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id CAA23204
	for <bio-software-list@hgmp.mrc.ac.uk>; Sat, 8 Jan 2000 02:10:08 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id CAA26246
	for bio-software-list@hgmp.mrc.ac.uk; Sat, 8 Jan 2000 02:10:07 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Stephen R. Lasky" <srlasky@cellworks.mbt.washington.edu>
X-Newsgroups: bionet.software
Subject: Re: phrap quality scores
Date: Sat, 08 Jan 2000 01:54:13 +0000
Organization: UW Department of Molecular Biotechnology
Lines: 30
Message-ID: <387698C5.EEA17FB@cellworks.mbt.washington.edu>
References: <slrn87cpdp.8ga.rgarcia@is05.fas.harvard.edu>
Reply-To: srlasky@u.washington.edu
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: nntp4.u.washington.edu 947296454 18486 (None) 140.142.17.39
X-Complaints-To: help@cac.washington.edu
X-Mailer: Mozilla 4.7 [en] (X11; U; Linux 2.2.5-15 i686)
X-Accept-Language: en
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

"Rachel M. Kadel-Garcia" wrote:
> 
> Does anyone here have an understanding of phrap quality scores
> beyond what's in the docs?  I'm trying to figure out how to
> assign similar quality scores to assemblies not done with phrap,
> and I'm resorting to spelunking in the source, but it's rough
> going.
> 
>                                                 Rachel


Phrap, I believe, is not the program assigning the quality scores. 
Phred is.  Phrap uses the phred quality scores to do its alignments.

Do you have the Phred docs? 

I presume that you don't have the chromats, otherwise you could run them
through phred and get the quality scores.

srlasky
-- 
Stephen R. Lasky, Ph.D.			#
University of Washington		#
Department of Molecular Biotechnology	#
HSB K336a box 357730			#
Seattle, WA, 98195 USA			#
email:	srlasky@u.washington.edu	#
Phone: 	206-616-5865			#
Fax:	206-685-7301			#
#########################################


From owner-bio-software@hgmp.mrc.ac.uk  Sat Jan  8 05:31:25 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 7422E17A61; Sat,  8 Jan 2000 05:31:24 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id FAA09643
	for <bio-software-list@hgmp.mrc.ac.uk>; Sat, 8 Jan 2000 05:31:21 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id FAA28606
	for bio-software-list@hgmp.mrc.ac.uk; Sat, 8 Jan 2000 05:31:20 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: rgarcia@is06.fas.harvard.edu (Rachel M. Kadel-Garcia)
X-Newsgroups: bionet.software
Subject: Re: phrap quality scores
Date: 8 Jan 2000 05:14:54 GMT
Organization: Harvard University, Cambridge, Massachusetts
Lines: 29
Message-ID: <slrn87dhv2.lqn.rgarcia@is06.fas.harvard.edu>
References: <slrn87cpdp.8ga.rgarcia@is05.fas.harvard.edu> <387698C5.EEA17FB@cellworks.mbt.washington.edu>
User-Agent: slrn/0.9.5.7 (UNIX)
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

In article <387698C5.EEA17FB@cellworks.mbt.washington.edu>, 
Stephen R. Lasky wrote:
>"Rachel M. Kadel-Garcia" wrote:
>> 
>> Does anyone here have an understanding of phrap quality scores
>> beyond what's in the docs?  I'm trying to figure out how to
>> assign similar quality scores to assemblies not done with phrap,
>> and I'm resorting to spelunking in the source, but it's rough
>> going.
>> 
>>                                                 Rachel
>
>
>Phrap, I believe, is not the program assigning the quality scores. 
>Phred is.  Phrap uses the phred quality scores to do its alignments.

Phred assigns quality scores to bases in individual reads.  Phrap uses
those quality scores and various things about the alignments to generate
consensus quality scores.

>Do you have the Phred docs? 
>
>I presume that you don't have the chromats, otherwise you could run them
>through phred and get the quality scores.

I have the phred docs and the chromat files, but that won't get me
consensus quality scores.

						Rachel


From owner-bio-software@hgmp.mrc.ac.uk  Sat Jan  8 18:33:44 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 3430217B52; Sat,  8 Jan 2000 18:33:44 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA13151
	for <bio-software-list@hgmp.mrc.ac.uk>; Sat, 8 Jan 2000 18:33:40 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA07972
	for bio-software-list@hgmp.mrc.ac.uk; Sat, 8 Jan 2000 18:33:39 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: shbowp@sdfsdf.com
X-Newsgroups: dk.edb.internet.webdesign.asp,bionet.software
Subject: LEGAL C`A`B`L`E TV D`E-S`C`R`A`M`B`L`E`R  5386
Lines: 58
Message-ID: <1oLd4.16215$J%4.9835@dfiatx1-snr1.gtei.net>
X-Trace: +4oQ4AIeWOwxwa8xWjO3SZi/BCP8xNPdr5/0bM8p0ZtUDSVe1yhhg/CkpmdH424OiMINrImYl7wT!SBy4ixv/y4KscJZ9u4w76yflcDCVx6Zxea2CIVecoyn1P8EcUhZXt9y/UJSyGWGmyDFp4oiPxT4L!jA==
X-Complaints-To: abuse@gte.net
X-Abuse-Info: Please be sure to forward a copy of ALL headers
X-Abuse-Info: Otherwise we will be unable to process your complaint properly
Distribution: world
Date: Sat, 08 Jan 2000 18:31:25 GMT
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

LEGAL C`A`B`L`E TV D`E-S`C`R`A`M`B`L`E`R

Want to watch Sporting Events?--Movies?--Pay-Per-View??....FREE!!!!

*This is the Famous R-O Shack TV D-e-s-c-r-a-m-b-l-e-r 
You can assemble it from Radio Shack parts for about $12 to $15.

We Send You: 
1, E-Z To follow Assembly Instructions. 
2. E-Z To read Original Drawings. 
3. Total Parts List.

**** PLUS SOMETHING NEW YOU MUST HAVE! ****
Something you can't do without.

THE UP-TO-DATE 6 PAGE REPORT: 
USING A D-E-S-C-R-A-M-B-L-E-R LEGALLY

Warning: You should not build a TV D-e-s-c-r-a-m-b-l-e-r 
without reading this report first.

You get the complete 6 page report
and instruction package including
the instruction plans, the easy to 
follow diagram, and most important 
of all the "Using a D`e`s`c`r`a`m`b`l`e`r
LEGALLY Report all for just--$10.00 

Fill out form below and send it,
along with your $10.00 payment to:

C.a.b.l.e.t.r.o.n FREE-TV
12187 S. Orange Blossom Trail #116
Orlando Fl 32837
 
(Cash, Check or Money Order.)
(Florida residents include 7% Florida State Sales Tax)
(All orders outside the U.S.A. add $5.00)


PRINT YOUR:

NAME______________________________________________________

ADDRESS___________________________________________________

CITY/STATE/ZIP____________________________________________

E-MAIl ADDRESS____________________________________________ 

We are NOT ASSOCIATED in any way with RADIO SHACK. 
Neither the design nor instructions were developed 
by, are sold by, or are endorsed by Radio Shack. 
Parts for this fine-tuning device are available 
at many electronics stores (including Radio Shack) 
This is not a Radio Shack product.
hmilobsdtxdimziqbgchrrskgtrgvtqzdokmntunvvyeysqhfncrh



From owner-bio-software@hgmp.mrc.ac.uk  Sat Jan  8 20:20:10 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 2E8B517A5D; Sat,  8 Jan 2000 20:20:09 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id UAA18060
	for <bio-software-list@hgmp.mrc.ac.uk>; Sat, 8 Jan 2000 20:20:07 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA09204
	for bio-software-list@hgmp.mrc.ac.uk; Sat, 8 Jan 2000 20:20:06 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
Reply-To: "SoftWarez Cafe" <uik87g@writemail.com>
From: "SoftWarez Cafe" <uik87g@writemail.com>
X-Newsgroups: bionet.software
Subject: Latest SoftWare For P.C. & Apple Mac
Date: Sat, 8 Jan 2000 16:20:10 -0000
Lines: 13
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2615.200
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200
Message-ID: <387766f3@news.jakinternet.co.uk>
X-Trace: 8 Jan 2000 16:33:55 GMT, user341.jakinternet.co.uk
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Send an email with "THE LIST" in the subject line to

auto.program.list@iname.com If not working send To uik87g@writemail.com

"SoftWare For P.C And Apple Macintosh"

...And we will send you a Full List with just about any Software package
that's going.
The software's supplied "strictly for backup purposes only" and is identical
to the original master copy. Cracks and serial numbers are supplied in case
your original licensing details have been mislaid.




From owner-bio-software@hgmp.mrc.ac.uk  Sun Jan  9 10:36:15 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id D016A17A56; Sun,  9 Jan 2000 10:36:14 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA07063
	for <bio-software-list@hgmp.mrc.ac.uk>; Sun, 9 Jan 2000 10:36:13 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA27561
	for bio-software-list@hgmp.mrc.ac.uk; Sun, 9 Jan 2000 10:36:12 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Andrea Hansen <webmaster@bioinformatik.de>
X-Newsgroups: bionet.software
Subject: Re: Looking for Cloning Software
Date: 09 Jan 2000 11:36:05 +0100
Lines: 19
Message-ID: <m0r9frpm5m.fsf@pc2-43.botanik.uni-duesseldorf.de>
References: <38721032.0@pfaff.ethz.ch>
X-Trace: fu-berlin.de 947414169 1476464 134.99.202.44 (16 [4974])
X-Newsreader: Gnus v5.5/XEmacs 20.4 - "Emerald"
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


> I am currently looking for (evaluating) DNA cloning software (e.g. for =
> manipulation of plasmids and fragments with correct terminior in silica =
> cloning , such as Clone Manager) for our PC platform. Apart from "Clone =
> Manager" I did not find very much in the field.=20

Hi Claude,
 you should look at our catalog:

http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software/Windows/

Best regards,
Andrea

-- 
Institut fuer Botanik III
Heinrich-Heine-Universitaet
Universitaetsstr.1         email : webmaster@bioinformatik.de 
40225 Duesseldorf          http://www.bioinformatik.de


From owner-bio-software@hgmp.mrc.ac.uk  Sun Jan  9 10:40:59 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id AFCE217A56; Sun,  9 Jan 2000 10:40:58 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA07279
	for <bio-software-list@hgmp.mrc.ac.uk>; Sun, 9 Jan 2000 10:40:57 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA27567
	for bio-software-list@hgmp.mrc.ac.uk; Sun, 9 Jan 2000 10:40:56 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Andrea Hansen <webmaster@bioinformatik.de>
X-Newsgroups: bionet.software
Subject: Re: seek software of promoter finding
Date: 09 Jan 2000 11:40:46 +0100
Lines: 15
Message-ID: <m0puvbplxt.fsf@pc2-43.botanik.uni-duesseldorf.de>
References: <3851C847.13C3B961@188.net>
X-Trace: fu-berlin.de 947414452 1476464 134.99.202.44 (16 [4974])
X-Newsreader: Gnus v5.5/XEmacs 20.4 - "Emerald"
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

hbzh@188.net (Haobin Zhao) writes:

> I am now doing research about gene clone and gene expression, I want a
> software to find the gene promoter.
Look at
http://www.bioinformatik.de/cgi-bin/browse/Catalog/Databases/Regulatory_Regions/

You will find programs for promotor prediction.

Andrea
-- 
Institut fuer Botanik III
Heinrich-Heine-Universitaet
Universitaetsstr.1         email : webmaster@bioinformatik.de 
40225 Duesseldorf          http://www.bioinformatik.de


From owner-bio-software@hgmp.mrc.ac.uk  Sun Jan  9 11:34:28 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 6488317B10; Sun,  9 Jan 2000 11:34:23 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA09652
	for <bio-software-list@hgmp.mrc.ac.uk>; Sun, 9 Jan 2000 11:34:09 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA28194
	for bio-software-list@hgmp.mrc.ac.uk; Sun, 9 Jan 2000 11:34:09 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "http://www.moler.co.uk" <Chris@Moler.co.uk>
X-Newsgroups: bionet.software
Subject: M o l e r !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Date: Sun, 9 Jan 2000 11:33:41 -0000
Organization: GXSN
Lines: 10
Message-ID: <859rnd$3as$1@gxsn.com>
X-Trace: 947417645 1NNUCNF1GE89DC393C gxsn.com
X-Complaints-To: abuse@gxsn.com
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2014.211
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk



--
-----------------------------------------------------------------
                         Moler Inc.
   Software for kids and computer retards!
               http://www.moler.co.uk
-----------------------------------------------------------------




From owner-bio-software@hgmp.mrc.ac.uk  Sun Jan  9 19:15:18 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 8D34817A43; Sun,  9 Jan 2000 19:15:17 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA00404
	for <bio-software-list@hgmp.mrc.ac.uk>; Sun, 9 Jan 2000 19:15:15 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA03787
	for bio-software-list@hgmp.mrc.ac.uk; Sun, 9 Jan 2000 19:15:14 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Todd Scheetz <todd-scheetz@uiowa.edu>
X-Newsgroups: bionet.software
Subject: Re: phrap quality scores
Date: Sun, 09 Jan 2000 13:07:22 -0600
Organization: The University of Iowa
Lines: 52
Message-ID: <3878DC6A.46CE3146@uiowa.edu>
References: <slrn87cpdp.8ga.rgarcia@is05.fas.harvard.edu> <387698C5.EEA17FB@cellworks.mbt.washington.edu> <slrn87dhv2.lqn.rgarcia@is06.fas.harvard.edu>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: flood.weeg.uiowa.edu 947444585 8856 128.255.22.155 (9 Jan 2000 19:03:05 GMT)
X-Complaints-To: usenet@news.uiowa.edu
X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.12-20 i686)
X-Accept-Language: en
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


Rachel,

I'm assuming you've got the phred generated sequence and quality files.
>From the limited testing I've done recently, with limited amounts of
overlapping sequence to keep the complexity down, here's the way it
appears to work.

1. If sequence in only one direction, the highest/best score is used.
2. If sequence in both directions, the best qualities from each
direction are added together.

However, this comes with a few caveats. Phrap brings the sequences
together in segments, so the highest quality value mention above is
really the quality value of that base within the segment chosen as the
representative. Also, I haven't quite figured out the quality given to
discordant bases. I haven't bothered digging into the source yet,
though. If I find out anything more, I'll let you know (if you'd like).

-Todd

"Rachel M. Kadel-Garcia" wrote:
> 
> In article <387698C5.EEA17FB@cellworks.mbt.washington.edu>,
> Stephen R. Lasky wrote:
> >"Rachel M. Kadel-Garcia" wrote:
> >>
> >> Does anyone here have an understanding of phrap quality scores
> >> beyond what's in the docs?  I'm trying to figure out how to
> >> assign similar quality scores to assemblies not done with phrap,
> >> and I'm resorting to spelunking in the source, but it's rough
> >> going.
> >>
> >>                                                 Rachel
> >
> >
> >Phrap, I believe, is not the program assigning the quality scores.
> >Phred is.  Phrap uses the phred quality scores to do its alignments.
> 
> Phred assigns quality scores to bases in individual reads.  Phrap uses
> those quality scores and various things about the alignments to generate
> consensus quality scores.
> 
> >Do you have the Phred docs?
> >
> >I presume that you don't have the chromats, otherwise you could run them
> >through phred and get the quality scores.
> 
> I have the phred docs and the chromat files, but that won't get me
> consensus quality scores.
> 
>                                                 Rachel


From owner-bio-software@hgmp.mrc.ac.uk  Sun Jan  9 23:19:04 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 73F1C17A5A; Sun,  9 Jan 2000 23:19:03 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id XAA20272
	for <bio-software-list@hgmp.mrc.ac.uk>; Sun, 9 Jan 2000 23:19:01 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id XAA15061
	for bio-software-list@hgmp.mrc.ac.uk; Sun, 9 Jan 2000 23:19:00 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: johns@ks.uiuc.edu (John Stone)
X-Newsgroups: bionet.software
Subject: Announce: VMD 1.4
Date: 9 Jan 2000 23:18:55 GMT
Organization: University of Illinois at Urbana-Champaign
Lines: 43
Message-ID: <slrn87i5qv.8le.johns@geneseo.ks.uiuc.edu>
User-Agent: slrn/0.9.6.2 (SunOS)
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


         VMD "Visual Molecular Dynamics" 1.4 Announcement
         ------------------------------------------------
The Theoretical Biophysics group at the Beckman Institute For Advanced  
Science and Technology, the University of Illinois (U-C), is proud to
announce the public release of VMD 1.4.  VMD is a package for the 
visualization and analysis of biomolecular systems.  This software is
distributed free of charge and includes source code, documentation,
and precompiled binaries for IBM, HP, Linux, Sun, and SGI Unix systems, 
as well as Microsoft Windows 95/98/NT.
The VMD documentation includes an installation guide, a users guide, and a 
programmers guide for interested researchers.  VMD also provides on-line 
help through the use of an external HTML viewer.  VMD development is 
supported by the NIH National Center for Research Resources.

A full description of VMD is available via the VMD WWW home page:
        http://www.ks.uiuc.edu/Research/vmd/

The authors request that any published work which utilizes VMD includes 
a reference to the VMD web page and/or the following reference:

  Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular
  Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.

The Theoretical Biophysics group encourages VMD users to be closely  
involved in the development process through reporting bugs, contributing  
fixes, periodical surveys and via other means.

We are eager to hear from you, and thank you for using our software!

                                                John Stone
                                                vmd@ks.uiuc.edu
                                                January 7, 2000


-- 

Theoretical Biophysics Group   Email: johns at ks.uiuc.edu
Beckman Institute              http://www.ks.uiuc.edu/~johns/
University of Illinois         Phone:  (217) 244-3349
405 N. Mathews  Ave              FAX:  (217) 244-6078 
Urbana, IL 61801, USA          Unix Is Good For You!!!



From owner-bio-software@hgmp.mrc.ac.uk  Mon Jan 10 09:27:19 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 6435A17A5E; Mon, 10 Jan 2000 09:27:19 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA26713
	for <bio-software-list@hgmp.mrc.ac.uk>; Mon, 10 Jan 2000 09:27:17 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA22171
	for bio-software-list@hgmp.mrc.ac.uk; Mon, 10 Jan 2000 09:27:16 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: dio60@goethe.de (TTV-01)
X-Newsgroups: bionet.software
Subject: For Your Information....FYI
Date: 10 Jan 2000 09:27:16 -0000
Organization: MRC Human Genome Mapping Project Resource Centre
Lines: 53
Message-ID: <200001103638WAA52773@utqtdjlb.ca>
X-Trace: niobium.hgmp.mrc.ac.uk 947496436 22169 193.62.192.80 (10 Jan 2000 09:27:16 GMT)
X-Complaints-To: news@hgmp.mrc.ac.uk
X-Received: from Argon.Mlink.NET (Argon.Mlink.NET [205.236.182.18])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA26697;
	Mon, 10 Jan 2000 09:27:13 GMT
X-Received: from publicor.ca (publicor.ca [209.104.113.131]) by Argon.Mlink.NET (8.8.8/8.8.2) with ESMTP id EAA02181; Mon, 10 Jan 2000 04:24:49 -0500 (EST)
X-Received: from dyral (206.229.193.133) by publicor.ca with SMTP (Eudora
 Internet Mail Server 2.2); Mon, 10 Jan 2000 04:24:15 -0500
X-To: dio60@goethe.de
X-Comments: Authenticated sender is <dio60@goethe.de>
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


To all of our recent email survery respondence we want to pass on some
important information. If you received this message in error we apologize. 

********************************WOW***************************************

GREAT OPPORTUNITY BIG PROFITS IN IMPORT & EXPORT!!!

Make money in the Import-Export business. Fantastic new way
to start your import-export business right from your own home.
The boom in selling import items to U.S. consumers is creating
unprecedented income opportunities. Begin without investing in
merchandise. The U.S. Government will help.

For information call 1-800-242-0363 Ext. 2358

********************************WOW***************************************

Pre-Enroll In Unique Business System; Homeowners Get Free $395 Value!

For the first 500 homeowners who call our  24-hour Home Business Hotline 
and pre-enroll into the Hottest Home Business sweeping America, we'll send 
you absolutely free the "Mortgage Manager" Software that will show you 
how to: * Save Thousands of Dollars on your home mortgage without increasing
your payment * Shorten your 30 year mortgage by 7-15 years without refinancing*
Build equity in your home 300% faster, and much more!  Just call our 24-hour 
Hotline and pre-enroll into a new & unique home-based business system with no 
money down. If you're not a homeowner, you can still pre-enroll for our home 
based business system!  Pre-enroll, and get the Mortgage Manager---a  $395
value absolutely free!  

Call to hear details, 1-800-242-0363 Ext. 1531 

********************************WOW***************************************

AS SEEN ON TV!!!

NEEDED:  5 - 10 People who desire $1,200 - $1,500 /month Part Time or 
$4,000 - $6,000 Full Time.  Work from home.  Full Support.  Fully Financed 
Opportunity.  Call for FREE recorded information. 

1-888-212-6385  (24 hours.)  

********************************WOW***************************************

We adhere to RESPONSIBLE Email Ethics 

This is a 1 Time Mailing,  no need to be removed Our 

software will automatically block you from  future mailings.

*******************************WOW****************************************
)t=


From owner-bio-software@hgmp.mrc.ac.uk  Mon Jan 10 13:24:15 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 1E08417A62; Mon, 10 Jan 2000 13:24:14 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA22256
	for <bio-software-list@hgmp.mrc.ac.uk>; Mon, 10 Jan 2000 13:24:13 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA25280
	for bio-software-list@hgmp.mrc.ac.uk; Mon, 10 Jan 2000 13:24:12 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Stefan Weckx <sweckx@uia.ua.ac.be>
X-Newsgroups: bionet.software
Subject: dataset
Date: Mon, 10 Jan 2000 14:29:09 +0100
Organization: Universiteit Antwerpen - Moleculaire Genetica
Lines: 12
Message-ID: <3879DEA5.1BC3B03E@uia.ua.ac.be>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: naxos.belnet.be 947510646 7818 143.169.254.1 (10 Jan 2000 13:24:06 GMT)
X-Complaints-To: abuse@belnet.be
X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.12-20 i686)
X-Accept-Language: en
X-Original-NNTP-Posting-Host: practicum1.uia.ac.be
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

To be able to compare some DNA assembly programs, I'm looking for raw
DNA sequences (abi format) from a shotgun cloning and the final assebled
sequence (BAC,..). It seems that it isn't possible to download this kind
of files from the web. Can somebody help us?

thanks
-- 
==============================================================================
Stefan Weckx				
University of Antwerp				
Belgium
==============================================================================


From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan 11 07:10:46 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id CF51F17AE7; Tue, 11 Jan 2000 07:10:44 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id HAA26789
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 11 Jan 2000 07:10:42 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA16412
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 11 Jan 2000 07:10:41 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: spam@127.0.0.1 (Bernard Murray, PhD)
X-Newsgroups: bionet.software
Subject: Re: dataset
Date: Mon, 10 Jan 2000 22:09:42 -0700
Organization: UCSF
Lines: 24
Message-ID: <spam-1001002209420001@macmac-2.ucsf.edu>
References: <3879DEA5.1BC3B03E@uia.ua.ac.be>
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

In article <3879DEA5.1BC3B03E@uia.ua.ac.be>, Stefan Weckx
<sweckx@uia.ua.ac.be> wrote:

> To be able to compare some DNA assembly programs, I'm looking for raw
> DNA sequences (abi format) from a shotgun cloning and the final assebled
> sequence (BAC,..). It seems that it isn't possible to download this kind
> of files from the web. Can somebody help us?

To get some ideas on creating a fake dataset you might want to
look at an earlier study;

Miller MJ & Powell JI (1994)
"A quantitative comparison of DNA sequence assembly programs."
J Comput Biol 1994 Winter;1(4):257-69 

They looked at a real dataset and used this to
design fake sets with different error levels.

   Bernard

-- 
Bernard P. Murray, PhD
bpmurray at cgl . ucsf . edu
Department of Cellular & Molecular Pharmacology, UCSF


From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan 11 07:33:33 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 28C1517A5A; Tue, 11 Jan 2000 07:33:32 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id HAA27799
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 11 Jan 2000 07:33:31 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA16645
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 11 Jan 2000 07:33:30 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Ken Beath <kjbeath@kagi.com>
X-Newsgroups: comp.sys.mac.scitech,sci.stat.edu,sci.stat.consult,bionet.software
Reply-To: kjbeat@kagi.com
Subject: [Ann] GLMStat (Macintosh) generalized linear models software
Message-ID: <110120001829443898%kjbeath@kagi.com>
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-transfer-encoding: 8bit
User-Agent: YA-NewsWatcher/4.2.6
Lines: 35
X-Trace: ozemail.com.au 947575960 203.108.150.188 (Tue, 11 Jan 2000 18:32:40 EST)
Organization: OzEmail Pty Ltd, Australia
Distribution: world
Date: Tue, 11 Jan 2000 18:29:44 +1100
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

GLMStat is a Macintosh-based (NOTE: currently no Windows or UNIX
version) statistical program for analysing generalised linear
models. Features of GLMStat are

 - spreadsheet style data entry
 - factors may be represented as either integers or strings (categories)
 - Normal, Poisson, Binomial and Gamma models with appropriate links
and  specification of convergence and aliasing parameters
 - Scatter and Residual plots
 - Matrix scatterplots
 - Box and Whisker plots
 - Frequency distribution histograms
 - Descriptive statistics.
 - Output of deviance, parameter estimates, residuals and parameter
correlations
 - Saving of data files complete with all model specifications.
 - printing of data, graph and results.
 - Missing values
 - Online Help (under the apple menu) and a brief User Manual.
 - includes example data files for most examples in two of the texts.
 - Individual licences available for $US25. 10 User Site Licences
$US100. Site licences $US200. World site licence $US500. Payment in $US
through Kagi Shareware.
 - Registration includes free upgrades to version 6.x

Unregistered copies are fully functional except that Save and Save As
are disabled and there are
some limitations on usage.
 
GLMStat is available for download at info-mac archives or from
   http://www.ozemail.com.au/~kjbeath/glmstat.html
   
   
Ken Beath
kjbeath@kagi.com


From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan 11 07:35:40 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 2053317A5A; Tue, 11 Jan 2000 07:35:39 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id HAA27943
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 11 Jan 2000 07:35:38 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA16758
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 11 Jan 2000 07:35:37 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Ken Beath <kjbeath@kagi.com>
X-Newsgroups: comp.sys.mac.scitech,sci.stat.edu,sci.stat.consult,bionet.software
Subject: cancel <110120001829443898%kjbeath@kagi.com>
Message-ID: <110120001832012118%kjbeath@kagi.com>
Control: cancel <110120001829443898%kjbeath@kagi.com>
User-Agent: YA-NewsWatcher/4.2.6
Lines: 1
X-Trace: ozemail.com.au 947576096 203.108.150.188 (Tue, 11 Jan 2000 18:34:56 EST)
Organization: OzEmail Pty Ltd, Australia
Distribution: world
Date: Tue, 11 Jan 2000 18:32:01 +1100
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

cancel <110120001829443898%kjbeath@kagi.com>


From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan 11 13:00:18 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 3067817A66; Tue, 11 Jan 2000 13:00:17 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA28261
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 11 Jan 2000 13:00:14 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA20801
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 11 Jan 2000 13:00:12 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Ivan Petrovic" <easyzip@softwarecenter.net>
X-Newsgroups: bionet.software
Subject: PowerArchiver 2000 v5.01 - !!! OLD NAME EASYZIP !!!
Date: Tue, 11 Jan 2000 13:58:24 +0100
Organization: HiNet
Lines: 80
Message-ID: <85f9e2$rrc$4@as102.tel.hr>
Mime-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
X-Trace: as102.tel.hr 947595522 28524 195.29.245.103 (11 Jan 2000 12:58:42 GMT)
X-Complaints-To: abuse@tel.hr
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2314.1300
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
PowerArchiver 2000 v5.01 [11th January 2000]
(old name EasyZip)
The most powerful Freeware Archive Utility that exists...
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

What is PowerArchiver?

PowerArchiver is the most powerful and totally FREE Archive
Utility... List of some features:
     * full built-in support for ZIP, CAB, LHA(LZH), TAR,
       TAR.GZ and BH (BlakHole) archives
     * built-in support for reading and extracting: RAR, ARJ,
       ARC, ACE, ZOO and GZip archives
    * full built-in support for XXE and UUE Internet encoded files
    * multiple disk spanning, powerful SFX archives, passwords,
       comments, renaming files within archive, installing archive,
       checking archive for viruses
     * integrated viewer with support for TXT, RTF, BMP,
        JPG(JPEG), ICO, WMF and EMF files, ...
     * complete integration with Windows Explorer: d&d, powerful
        Explorer Shell Extensions, ...
     * tool for converting between archive formats  (CAB ->
        LHA, ...), tool for splitting single ZIP archive, tool for
        detecting  archive type, ...
     * great interface similar to other popular archive utilities with two
        modes of viewing archive (Classic &  Explorer style), integrated
        file browser, ...
     * detailed help in new MS HTML Help format with the tutorial for
       beginners, ...
    * and many, many more useful and powerful features...

So try out this great utility.

What's new?

    Changes in this version --> EasyZip renamed  to  PowerArchiver,
added  support for writing TAR and TAR.GZ archives, internal viewer
now  beside TXT files supports RTF, BMP, ICO, WMF, EMF and
JPG (JPEG) files, tool for detecting archive format, selecting custom
toolbar buttons now available using "Small buttons", small misc
features  and many, many bug fixes...
    For detailed list of new features and bug  fixes  please  visit
PowerArchiver Forum at http://ipsoft.cjb.net

Support:

    PowerArchiver and more and more information about PowerArchiver
 you can find at:

            http://ipsoft.cjb.net

    and my e-mail address is:

            powerarc@ipsoft.cjb.net

Thanks in advance...
Ivan Petrovic



--
___________________________________________________________
  PowerArchiver 2000 - The most powerful and Free Archive
  Utility  for  Windows  95/98/NT/2000  that has built-in
  support for many, many formats: ZIP, CAB, LHA, BH, ARJ,
  RAR, ACE, ARC, ZOO, TAR, GZ, XXE, UUE...
-----------------------------------------------------------
  ArchiveUtilities - 2  Free console programs with source
  in Borland Delphi
    ArcComp - compresses to ZIP, CAB,  LHA  and BH
    ArcExt  - extracts from ZIP, RAR, ARJ, CAB, LHA, ARC,
              ACE, GZIP, TAR, UUE and ZOO
  * * * * * * * * * * * * * * * * * * * * * * * * * * * *
                  http://ipsoft.cjb.net
                ivanpetrov@ipsoft.cjb.net
  * * * * * * * * * * * * * * * * * * * * * * * * * * * *





From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan 11 14:20:28 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 2B88817A66; Tue, 11 Jan 2000 14:20:27 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA07082
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 11 Jan 2000 14:20:22 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA21840
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 11 Jan 2000 14:20:21 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Soeren W. Rasmussen" <swr@crc.dk>
X-Newsgroups: bionet.software
Subject: SAGE analysis with DNATools
Date: Tue, 11 Jan 2000 15:13:53 +0100
Organization: UNI-C
Lines: 32
Message-ID: <387B3AA0.348B4492@crc.dk>
Mime-Version: 1.0
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit
X-Trace: news.net.uni-c.dk 947600216 29570 130.226.182.97 (11 Jan 2000 14:16:56 GMT)
X-Complaints-To: usenet@news.net.uni-c.dk
X-Mailer: Mozilla 4.7 [en] (Win95; I)
X-Accept-Language: en
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Dear DNATools user,

In case you use the SAGE functions (extract tags, tag file tools and
analysis functions) it might interest you to know that it is now
possible to im- and export sage tag files in the same format as is used
by NCBI (http://www.ncbi.nlm.nih.gov/SAGE/). The latest release of
DNATools, 5.1.653, also allows you to load SAGEmap files for identifying
your tags - and contains a function which let you create a SAGE map file
from your own annotated sequences. Most of the SAGE routines have been
optimised and now run a bit faster. Remember, however, that you still
need other, more sophisticated/powerful programs for analysis of very
large data set. We routinely use the programs for tag files of about
20,000 tags.

Please remember that comments and ideas are always welcome.

Regards


Soeren

--
Dr. scient. Søren W. Rasmussen
Carlsberg Laboratory, Department of Physiology
10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark
Phone  45 33275230/45 36162259, Fax 45 33274766
swr@crc.dk, http://www.crc.dk/phys/

DNATools sequencing software:
http://www.crc.dk/phys/dnatools.htm




From owner-bio-software@hgmp.mrc.ac.uk  Tue Jan 11 22:10:10 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id E390017A86; Tue, 11 Jan 2000 22:10:09 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA18011
	for <bio-software-list@hgmp.mrc.ac.uk>; Tue, 11 Jan 2000 22:10:08 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA05885
	for bio-software-list@hgmp.mrc.ac.uk; Tue, 11 Jan 2000 22:10:07 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Stephen R. Lasky" <srlasky@cellworks.mbt.washington.edu>
X-Newsgroups: bionet.software
Subject: Re: phrap quality scores
Date: Tue, 11 Jan 2000 21:50:18 +0000
Organization: UW Department of Molecular Biotechnology
Lines: 42
Message-ID: <387BA59A.B13AAFA2@cellworks.mbt.washington.edu>
References: <slrn87cpdp.8ga.rgarcia@is05.fas.harvard.edu> <387698C5.EEA17FB@cellworks.mbt.washington.edu> <slrn87dhv2.lqn.rgarcia@is06.fas.harvard.edu>
Reply-To: srlasky@u.washington.edu
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: nntp4.u.washington.edu 947627420 16100 (None) 140.142.17.35
X-Complaints-To: help@cac.washington.edu
X-Mailer: Mozilla 4.7 [en] (X11; U; Linux 2.2.5-15 i686)
X-Accept-Language: en
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

"Rachel M. Kadel-Garcia" wrote:
> 
> In article <387698C5.EEA17FB@cellworks.mbt.washington.edu>,
> Stephen R. Lasky wrote:
> >"Rachel M. Kadel-Garcia" wrote:
> >>
> >> Does anyone here have an understanding of phrap quality scores
> >> beyond what's in the docs?  I'm trying to figure out how to
> >> assign similar quality scores to assemblies not done with phrap,
> >> and I'm resorting to spelunking in the source, but it's rough
> >> going.
> >>
> >>                                                 Rachel
> >
> >
> >Phrap, I believe, is not the program assigning the quality scores.
> >Phred is.  Phrap uses the phred quality scores to do its alignments.
> 
> Phred assigns quality scores to bases in individual reads.  Phrap uses
> those quality scores and various things about the alignments to generate
> consensus quality scores.
> 
>

Sorry, you are correct.  Phrap does assign a quality score for the
concensus sequence based on the quality of the raw data (phred q score)
and the extent of confirmation of the base by other reads.

I do not know how to deconvolute that score.

srl

-- 
Stephen R. Lasky, Ph.D.			#
University of Washington		#
Department of Molecular Biotechnology	#
HSB K336a box 357730			#
Seattle, WA, 98195 USA			#
email:	srlasky@u.washington.edu	#
Phone: 	206-616-5865			#
Fax:	206-685-7301			#
#########################################


From owner-bio-software@hgmp.mrc.ac.uk  Wed Jan 12 13:57:53 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 6A91617AAC; Wed, 12 Jan 2000 13:57:52 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA05286
	for <bio-software-list@hgmp.mrc.ac.uk>; Wed, 12 Jan 2000 13:57:49 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA17198
	for bio-software-list@hgmp.mrc.ac.uk; Wed, 12 Jan 2000 13:57:48 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Patricia Rodriguez-Tome <tome@sol6.ebi.ac.uk>
X-Newsgroups: bionet.software
Subject: CORBA workshops at the EBI
Date: 12 Jan 2000 13:57:47 +0000
Organization: EBI - European Bioinformatics Institute
Lines: 34
Message-ID: <wc901v75pg.fsf@sol6.ebi.ac.uk>
X-Trace: niobium.hgmp.mrc.ac.uk 947685468 17071 193.62.196.160 (12 Jan 2000 13:57:48 GMT)
X-Complaints-To: news@hgmp.mrc.ac.uk
X-Newsreader: Gnus v5.2.25/XEmacs 20.0
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk




The EBI will run 2 series of CORBA workshops

CORBA programming : 25-28 january 2000 and 13-15 March 2000

Advanced CORBA programming : 24-26 May 2000 and 4-6 July 2000

More information about the agenda and costs (sorry we do not have yet any 
funding for these workshops ) is available at:
http://corba.ebi.ac.uk/courses

Only the first 2 workshops pages are up. January is open only to
European participants , March is open to all.
In February, after the first workshop, the second series of pages will 
come up.


Please pass this information around for those you think might be interested. 
March and May workshops might be cancelled if there are not enough attendees,
 so it would be good to give us  a feedback if anyone plans to attend.

Cheers

Pat
-- 
=======================================================================
Dr. Patricia Rodriguez-Tome		| URL:  http://www.ebi.ac.uk
R & D Coordinator - Team Leader
The EMBL Outstation, Hinxton - The European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton	| Tel:	+44 (0)1223 494 409
Cambridge CB10 1SD, UK			| Fax:	+44 (0)1223 494 468
========================================================================


From owner-bio-software@hgmp.mrc.ac.uk  Wed Jan 12 18:05:07 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id E8B2B17A56; Wed, 12 Jan 2000 18:05:06 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA05818
	for <bio-software-list@hgmp.mrc.ac.uk>; Wed, 12 Jan 2000 18:05:05 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA20433
	for bio-software-list@hgmp.mrc.ac.uk; Wed, 12 Jan 2000 18:05:03 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: j3@post.com (J3)
X-Newsgroups: bionet.software
Subject: Re: Looking for Cloning Software
Date: Wed, 12 Jan 2000 18:03:07 GMT
Organization: Network for Education and Research in Oregon
Lines: 17
Message-ID: <387cc176.70391227@news.orst.edu>
References: <38721032.0@pfaff.ethz.ch> <m0r9frpm5m.fsf@pc2-43.botanik.uni-duesseldorf.de>
Reply-To: j3@post.com
X-Trace: news.NERO.NET 947700187 27605 128.193.115.165 (12 Jan 2000 18:03:07 GMT)
X-Complaints-To: abuse@nero.net
X-Newsreader: Forte Free Agent 1.11/32.235
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

I strongly suggest pDRAW32 because its free (well, really beerware).
If you can afford to spend some money then go with Redasoft's Plasmid
v1.1.

Just my $0.02 worth as a grad student of molecular biology.

- J3 -


____________________________________________

Want more from your time online?  Try these:

1) http://www.getpaid4.com/?jwps3
2) http://www.alladvantage.com/go.asp?refid=HED306
3) http://www.utopiad.com/member/getPaid?refId=288529
4) http://www.spedia.net/cgi-bin/dir/tz.cgi?run=show_svc&fl=8&vid=505405


From owner-bio-software@hgmp.mrc.ac.uk  Thu Jan 13 17:02:29 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 1230517A67; Thu, 13 Jan 2000 17:02:28 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA11055
	for <bio-software-list@hgmp.mrc.ac.uk>; Thu, 13 Jan 2000 17:02:26 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA16589
	for bio-software-list@hgmp.mrc.ac.uk; Thu, 13 Jan 2000 17:02:26 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: hh645@hotmail.com
X-Newsgroups: bionet.software
Subject: Need More Money? Need Health Benefits?
Date: 13 Jan 2000 17:02:24 -0000
Organization: MRC Human Genome Mapping Project Resource Centre
Lines: 32
Message-ID: <200001131702.RAA11035@hgmp.mrc.ac.uk>
X-Trace: niobium.hgmp.mrc.ac.uk 947782945 16587 193.62.192.80 (13 Jan 2000 17:02:25 GMT)
X-Complaints-To: news@hgmp.mrc.ac.uk
X-Received: from pmserver.pm-partner.de ([62.156.176.114])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with SMTP id RAA11035;
	Thu, 13 Jan 2000 17:02:21 GMT
X-Received: from lkj by pmserver.pm-partner.de (AppleShare IP Mail Server 6.1) id 41537 via TCP with SMTP; Thu, 13 Jan 2000 13:35:13 +0200
X-To: vy645@hotmail.com
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


Need Serious Cash During The Holiday Season?
Sell 3 easy products in your spare time and 
enjoy Dental/Vision and Pharmacy Benefits!  
Great for Sales Professionals, MLM'ers, Business Owners,
Insurance Salesmen, Homakers!
Call Today For More Information and join a company 
which has experienced 10,000% growth since 1991
Call Kurt at Mark L. Simmons & Associates at
1-888-522-7585. Call Now!!
P.S. You can do this full time and earn serious cash!!

Do not hit reply to this message,
in order to be removed send email to yah12@freei.net
and type remove in the subject line








         lknklkln





jgjhgjhgjhgjhg

---


From owner-bio-software@hgmp.mrc.ac.uk  Fri Jan 14 00:11:38 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 7822B17A4E; Fri, 14 Jan 2000 00:11:37 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id AAA18725
	for <bio-software-list@hgmp.mrc.ac.uk>; Fri, 14 Jan 2000 00:11:35 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id AAA00099
	for bio-software-list@hgmp.mrc.ac.uk; Fri, 14 Jan 2000 00:11:34 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
Reply-To: "SoftWarez Cafe" <uik87g@writemail.com>
From: "SoftWarez Cafe" <uik87g@writemail.com>
X-Newsgroups: bionet.software
Subject: Latest SoftWare For P.C. & Apple Mac
Date: Thu, 13 Jan 2000 21:23:08 -0000
Lines: 14
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2615.200
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200
Message-ID: <387e459b@news.jakinternet.co.uk>
X-Trace: 13 Jan 2000 21:37:31 GMT, user286.jakinternet.co.uk
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Send an email with "THE LIST" in the subject line to

auto.program.list@iname.com If not working send To uik87g@writemail.com

"SoftWare For P.C And Apple Macintosh"

...And we will send you a Full List with just about any Software package
that's going.
"strictly for backup purposes only" and is identical to the original master
copy.






From owner-bio-software@hgmp.mrc.ac.uk  Fri Jan 14 03:02:08 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 7480A17A4E; Fri, 14 Jan 2000 03:02:07 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id DAA26930
	for <bio-software-list@hgmp.mrc.ac.uk>; Fri, 14 Jan 2000 03:02:05 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id DAA02113
	for bio-software-list@hgmp.mrc.ac.uk; Fri, 14 Jan 2000 03:02:04 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: expomed@mindspring.com (MARTY THOMAS)
X-Newsgroups: bionet.software
Subject: Human Anatomy Program Updated
Date: 14 Jan 2000 03:01:36 GMT
Organization: Your Organization
Lines: 36
Message-ID: <85m3ig$dl4$4@nntp3.atl.mindspring.net>
Mime-Version: 1.0
Content-Type: Text/Plain; charset=US-ASCII
X-Newsreader: WinVN 0.99.8 (x86 32bit)
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


Gold Standard Multimedia Human Anatomy

Human Anatomy is an interactive, HTML based, cadaveric dissection 
tutorial. Designed to be used as a comprehensive supplement to the 
gross lab, this program takes the student step-by-step through 
dissection procedures using the world's largest collection of 
cadaveric photographs, hundreds of hand-drawn illustrations, 
and photos from models and skeletons.

In the practice mode, students can quiz themselves 
with the 4,700 multiple choice test questions and receive 
immediate feedback. Human Anatomy's point-and-click
interface supports all learning syles and teaching efficiency.

*14,000 references to over 6,000 cadaveric photographs.
*3D icons illustrating the orientation and field of 
view of the photos.
*Chapter and page references to frequently-used anatomy atlases: 
Netter's Grant's and Rohen/Yokochi.
*Over 4,700 quiz questions featuring immediate feedback and 
links back to the tutorial for review.
*Image enlargement to full screen size.
*Hundreds of hand-drawn illustrations with links to cadaveric photographs.
*Find feature locates any structure easily.
*Browser included.

http://www.expomed.com/humanat.htm 
http://www.visualman.com/gsm/humanat.htm
-- 
/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
Martin Thomas, expomed@mindspring.com
http://www.onsitedrugtesting.com/ Onsite Drug Testing
http://www.expomed.com/ Personal Protection Products
http://www.visualman.com/ Educational Software



From owner-bio-software@hgmp.mrc.ac.uk  Fri Jan 14 03:41:50 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 522D117A4E; Fri, 14 Jan 2000 03:41:50 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id DAA28497
	for <bio-software-list@hgmp.mrc.ac.uk>; Fri, 14 Jan 2000 03:41:48 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id DAA02585
	for bio-software-list@hgmp.mrc.ac.uk; Fri, 14 Jan 2000 03:41:46 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Mike Jones" <Mjones@jonestown.org>
Subject: Charting / Data Graphics For Windows
Date: Thu, 13 Jan 2000 21:36:31 -0600
Lines: 35
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2615.200
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200
Message-ID: <e8bsAEkX$GA.268@cpmsnbbsa02>
X-Newsgroups: bionet.software
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

www.clickitgraph.com

Rated 5 Stars by ZDNET -
http://hotfiles.zdnet.com/cgi-bin/texis/swlib/hotfiles/info.html?fcode=0012P
E&b=

ClickIt Graph is state of the art 32 bit data graphics software for Windows®
95, 98 and NT 4.0. ClickIt Graph is a user friendly full featured data
graphics package that offers over 23 different graph types for business,
engineering and science  presentations. Data is input into a database format
compatible with Microsoft Access® that allows for the ease of use, data
import, and export between different application formats. ClickIt Graph also
supports linking with Microsoft Word® and PowerPoint® 97 and 2000. Transfer
of ClickIt Graph drawn graphs to a Word® document or PowerPoint®
presentation in a consistent presentation quality is as easy as pressing an
F key. Save graphs drawn with ClickIt Graph in a keyword driven database for
fast retrieval of your graphical information.

ClickIt Graph supports 23 different two and three-dimensional chart types
including line, linear-logarithmic, logarithmic-linear,
logarithmic-logarithmic, scatter, 3D scatter, bar, 3D bar, pie, 3D pie, 3D
tape, 3D surface, polar, area, 3D area, box-whisker, bubble, candlestick,
open-high-low-close, high-low-close, gantt, and data bound line. CLickIt
Graph supports linear regression, polynomial, logarithmic, exponential,
power, inverse power and spline curve fitting. Best fit, mean, maximum,
minimum and standard deviation lines are available for scatter and line
graph types.  Up to 9th order polynomial functions are supported. Regression
equations for line, scatter, linear-logarithmic, logarithmic-logarithmic,
logarithmic-linear, polynomial, power, exponential and inverse power
functions are output to the graph legend and a text file. Error bars are
available for most graph types.






From owner-bio-software@hgmp.mrc.ac.uk  Fri Jan 14 14:01:37 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id B780417ACB; Fri, 14 Jan 2000 14:01:36 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA22720
	for <bio-software-list@hgmp.mrc.ac.uk>; Fri, 14 Jan 2000 14:01:33 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA10171
	for bio-software-list@hgmp.mrc.ac.uk; Fri, 14 Jan 2000 14:01:32 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: JL Oliver <oliver@ugr.es>
X-Newsgroups: bionet.software
Subject: bioinformatics meeting
Date: Fri, 14 Jan 2000 14:38:32 +0100
Organization: Universidad de Granada
Lines: 2
Message-ID: <387F26D8.E9683A87@ugr.es>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: mercurio.cica.es 947857051 3001 150.214.61.117 (14 Jan 2000 13:37:31 GMT)
X-Complaints-To: news@cica.es
X-Mailer: Mozilla 4.7 [en] (Win98; I)
X-Accept-Language: en
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


http://www.es.embnet.org/~biocomp/bioinfo2000/


From owner-bio-software@hgmp.mrc.ac.uk  Fri Jan 14 16:40:06 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id DCB3D17AAB; Fri, 14 Jan 2000 16:40:05 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA09761
	for <bio-software-list@hgmp.mrc.ac.uk>; Fri, 14 Jan 2000 16:40:03 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA12106
	for bio-software-list@hgmp.mrc.ac.uk; Fri, 14 Jan 2000 16:40:02 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Ira Haron <iraharon@erols.com>
X-Newsgroups: sci.image.processing,comp.graphics.apps.photoshop,comp.sys.mac.scitech,sci.bio.technology,sci.materials,sci.techniques.microscopy,alt.image.medical,bionet.software,comp.graphics.misc,comp.software.measurement
Subject: help find this book
Date: Fri, 14 Jan 2000 11:22:15 -0500
Lines: 45
Message-ID: <387F4D37.8EECC844@erols.com>
Reply-To: iraharon@erols.com
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: qWjLrVrazKhnsZwqwN+D5uCl7FZf4EuPNELW0s4T8M8=
X-Complaints-To: abuse@rcn.com
X-Accept-Language:  en,pdf
X-Mailer:  Mozilla 4.7 [en] (Win98; I)
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


Group,

Can anyone help me find this book/manual/pamphlet?

***************************************************

  Name:
  Image Processing Tutor (IPT).


  Info on publisher:
  Copyright Unitron Services
  Flat 104
  Brigade Links, 54/1
  Sesharipuram
  1st Main Road
  Bangalore - 560 020
  Phones 36 35 32 336 10 58


  Physical description:
  Spiral bound, Approximately 120 pages
  Ver 1.1, Release Date November 1, 1994


  Quoted from first page:
"Getting Started:
Image Processing Tutor is a work book cum software combination to
introduce the concepts Digital Image Processing through experiments done

with a PC equipped with an M8 frame grabber board ..."

**************************************************

thank you for your time and courtesy,

ira
iraharon@erols.com








From owner-bio-software@hgmp.mrc.ac.uk  Sat Jan 15 08:49:18 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 186A617B33; Sat, 15 Jan 2000 08:49:17 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA14411
	for <bio-software-list@hgmp.mrc.ac.uk>; Sat, 15 Jan 2000 08:49:16 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA01860
	for bio-software-list@hgmp.mrc.ac.uk; Sat, 15 Jan 2000 08:49:15 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: main@mainengineering.com (Lou Main)
X-Newsgroups: bionet.software
Subject: New Security Product
Date: 15 Jan 2000 08:49:15 -0000
Organization: Main Engineering Corporation
Lines: 60
Message-ID: <947897588@cx989383-a.pwy1.sdca.home.com>
Mime-Version: 1.0
Content-Type: multipart/mixed; boundary="947897588762B0018=="
Content-Transfer-Encoding: 7bit
X-Trace: niobium.hgmp.mrc.ac.uk 947926155 1858 193.62.192.80 (15 Jan 2000 08:49:15 GMT)
X-Complaints-To: news@hgmp.mrc.ac.uk
X-Received: from lh2.rdc1.sdca.home.com (ioracle@ha2.rdc1.sdca.home.com [24.0.3.67])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA14404
	for <bio-soft@net.bio.net>; Sat, 15 Jan 2000 08:49:13 GMT
X-Received: from cx989383-a.pwy1.sdca.home.com ([24.0.43.118])
          by lh2.rdc1.sdca.home.com (InterMail v4.01.01.00 201-229-111)
          with SMTP
          id <20000115084911.EDLU1336.lh2.rdc1.sdca.home.com@cx989383-a.pwy1.sdca.home.com>
          for <bio-soft@net.bio.net>; Sat, 15 Jan 2000 00:49:11 -0800
X-To: bio-soft@hgmp.mrc.ac.uk
X-Reply-To: main@mainengineering.com
X-Priority: 3
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk


--947897588762B0018==
Content-Type: text/plain
Content-Transfer-Encoding: quoted-printable

If you own a nice auto or plan on buying one this year and want
to keep it, you need to read the following information, if not
please delete.

Main Engineering Corporation, a unique vehicle security
manufacturer with several patented systems to it's credit
advocating "total immobility", is presently launching their
newest product.

The HotSeat is the newest, most protective, completely automatic
anti-car jacking and security system to ever hit the market.  A
unique system providing maximum safety to the driver/owner and
promotes a "No High Speed Pursuit" scenario.  This alone saves
your customers and their insurance companies thousands of
dollars from property damage and bodily injury lawsuits.  Easy
to install, undetectable by the thief, impossible to shutdown
after the automatic timing sequence has started and convenience
for the customer.

Some Features of the HotSeat are:
*  Completely automatic, no driver intervention
*  Impossible to become part of any "High Speed Pursuit"
*  Provides a safety net for the victim
*  Vehicle - easy recovery - within sight
*  Inexpensive to own
*  Insurance savings
*  Also used as a security system
*  Provides a "No Start" alarm-siren with theft attempts
*  Undetectable by the thief
*  No false alarms to contend with
*  Cannot accidently activate system
*  Easy to install

Main Engineering is presently seeking individuals
that want to keep what they own.  We are setting up installation
facilities around the US and abroad that want to get in on the
ground floor of this new and exciting product.

If you would like more detailed information please go to our
website at http://www.mainengineering.com/index_1.htm or respond
by email to main@mainengineering.com.  You can also phone us
toll free at 877-748-5340.

We build only the finest security systems available anywhere,
we do not make alarms.

Thank you for the time you have given this information and we
hope to hear from you soon.

Best regards,
Lou Main, CEO
Main Engineering Corporation

--947897588762B0018==--
---


From owner-bio-software@hgmp.mrc.ac.uk  Sat Jan 15 18:35:07 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id C6E0A17A43; Sat, 15 Jan 2000 18:35:06 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA10079
	for <bio-software-list@hgmp.mrc.ac.uk>; Sat, 15 Jan 2000 18:35:05 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA08667
	for bio-software-list@hgmp.mrc.ac.uk; Sat, 15 Jan 2000 18:35:04 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "S.W. Rasmussen" <swr@crc.dk>
X-Newsgroups: bionet.software
Subject: Re: SAGE analysis with DNATools
Date: Sat, 15 Jan 2000 19:25:36 +0000
Organization: UNI-C
Lines: 17
Message-ID: <3880C9B0.8A074269@crc.dk>
References: <387B3AA0.348B4492@crc.dk>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: news.net.uni-c.dk 947960602 14106 130.226.184.128 (15 Jan 2000 18:23:22 GMT)
X-Complaints-To: usenet@news.net.uni-c.dk
X-Mailer: Mozilla 4.5 [en] (WinNT; I)
X-Accept-Language: en
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Dear DNATools user,

I may have been a bit too quick publishing the updated SAGE functions.
Unfortunately, there is a number of bugs in 5.1.653 (in the SAGE functions, the
remaining functions were not changed in 563). I have corrected them all (I hope)
in revision 654 which will be available for downloading monday, 17.1. Sorry.

Regards

Soeren

-- 
Soeren W. Rasmussen, Dr. scient.
Department of Physiology
Carlsberg Laboratory
Copenhagen, Denmark
swr@crc.dk, http://www.crc.dk/phys


From owner-bio-software@hgmp.mrc.ac.uk  Sun Jan 16 01:36:14 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 8ED0F17A5B; Sun, 16 Jan 2000 01:36:13 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id BAA06463
	for <bio-software-list@hgmp.mrc.ac.uk>; Sun, 16 Jan 2000 01:36:11 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id BAA21884
	for bio-software-list@hgmp.mrc.ac.uk; Sun, 16 Jan 2000 01:36:10 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: greg@franklin.burnham-inst.org (Dr. Greg Quinn)
X-Newsgroups: bionet.software
Subject: Functional equivalent of GCG Findpatterns?
Date: 16 Jan 2000 01:39:43 GMT
Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE
Lines: 5
Message-ID: <85r7gv$hso$1@franklin.ljcrf.edu>
X-Newsreader: TIN [UNIX 1.3 950824BETA PL0]
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Hi;
Does anyone know of a publicly available functional equivalent of the GCG 
FindPatterns program?
Thanks
Greg


From owner-bio-software@hgmp.mrc.ac.uk  Sun Jan 16 13:33:18 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id BD21517A68; Sun, 16 Jan 2000 13:33:17 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA08095
	for <bio-software-list@hgmp.mrc.ac.uk>; Sun, 16 Jan 2000 13:33:16 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA00341
	for bio-software-list@hgmp.mrc.ac.uk; Sun, 16 Jan 2000 13:33:15 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Keith James <kdj@fes1.sanger.ac.uk>
X-Newsgroups: bionet.software
Subject: Re: Functional equivalent of GCG Findpatterns?
Date: 16 Jan 2000 13:33:14 +0000
Organization: MRC Human Genome Mapping Project Resource Centre
Lines: 24
Message-ID: <sc4ogamrvj9.fsf@fes1.sanger.ac.uk>
References: <85r7gv$hso$1@franklin.ljcrf.edu>
Mime-Version: 1.0 (generated by tm-edit 7.106)
Content-Type: text/plain; charset=NIL
X-Trace: niobium.hgmp.mrc.ac.uk 948029594 339 193.60.84.165 (16 Jan 2000 13:33:14 GMT)
X-Complaints-To: news@hgmp.mrc.ac.uk
X-Newsreader: Gnus v5.5/Emacs 20.3
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

>>>>> "Greg" == Greg Quinn <greg@franklin.burnham-inst.org> writes:

    Greg> Hi; Does anyone know of a publicly available functional
    Greg> equivalent of the GCG FindPatterns program?

The EMBOSS program fuzznuc will search sequences or databases for
arbitrary, short patterns in a similar manner to findpatterns. It
allows a number of mismatches to be supplied.

The output is more terse than findpatterns, but on the other hand
there are no arbitrary limits on the length of sequence to be searched
or number of hits reported.

fuzznuc is part of the EMBOSS package which already covers much of
GCG's functionality. It's homepage is at:

http://www.sanger.ac.uk/Software/EMBOSS/

hth

-- 

Keith James  --  kdj@sanger.ac.uk  --  http://www.sanger.ac.uk/Users/kdj
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA


From owner-bio-software@hgmp.mrc.ac.uk  Mon Jan 17 11:48:21 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id B696417A8D; Mon, 17 Jan 2000 11:48:19 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA09750
	for <bio-software-list@hgmp.mrc.ac.uk>; Mon, 17 Jan 2000 11:48:17 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA24394
	for bio-software-list@hgmp.mrc.ac.uk; Mon, 17 Jan 2000 11:48:15 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Peter Rice <pmr@sanger.ac.uk>
X-Newsgroups: bionet.software
Subject: Re: Functional equivalent of GCG Findpatterns?
Date: 17 Jan 2000 11:48:13 +0000
Organization: The Sanger Centre
Lines: 28
Message-ID: <sub3drw537m.fsf@europa.sanger.ac.uk>
References: <85r7gv$hso$1@franklin.ljcrf.edu> <sc4ogamrvj9.fsf@fes1.sanger.ac.uk>
X-Trace: niobium.hgmp.mrc.ac.uk 948109694 24387 193.62.207.78 (17 Jan 2000 11:48:14 GMT)
X-Complaints-To: news@hgmp.mrc.ac.uk
X-Newsreader: Gnus v5.5/Emacs 20.3
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Keith James <kdj@fes1.sanger.ac.uk> writes:

> >>>>> "Greg" == Greg Quinn <greg@franklin.burnham-inst.org> writes:
> 
>     Greg> Hi; Does anyone know of a publicly available functional
>     Greg> equivalent of the GCG FindPatterns program?
> 
> The EMBOSS program fuzznuc will search sequences or databases for
> arbitrary, short patterns in a similar manner to findpatterns. It
> allows a number of mismatches to be supplied.
> 
> The output is more terse than findpatterns, but on the other hand
> there are no arbitrary limits on the length of sequence to be searched
> or number of hits reported.

It would be relatively easy to extend the output of fuzznuc
if users have particular needs.

One option under active consideration, for example, is to report the
hits in feature format (currently GFF, but soon also EMBL/Genbank
feature format and SwissProt for fuzzpro)

-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr@sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/


From owner-bio-software@hgmp.mrc.ac.uk  Mon Jan 17 16:08:07 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 0147617B10; Mon, 17 Jan 2000 16:08:06 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA28892
	for <bio-software-list@hgmp.mrc.ac.uk>; Mon, 17 Jan 2000 16:08:02 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA27645
	for bio-software-list@hgmp.mrc.ac.uk; Mon, 17 Jan 2000 16:07:59 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "SteoBio" <stia_g@yahoo.com>
X-Newsgroups: bionet.software
Subject: Multi analyst
Date: Mon, 17 Jan 2000 17:06:16 +0100
Organization: Tiscali Spa
Lines: 8
Message-ID: <85veoo$mtk$1@lacerta.tiscalinet.it>
X-Trace: lacerta.tiscalinet.it 948125272 23476 62.10.34.136 (17 Jan 2000 16:07:52 GMT)
X-Complaints-To: newsadmin@tiscali.it
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2014.211
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

Recently, i have downloaded this program from the Bio-Rad ftp server, but it
doesn't run because needs hardware key. Who knows the program? is there a
way to make it run (crack)?
Thanks

Stefano




From owner-bio-software@hgmp.mrc.ac.uk  Mon Jan 17 19:11:28 2000
Return-Path: <owner-bio-software@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 4BED517A65; Mon, 17 Jan 2000 19:11:27 +0000 (GMT)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA19409
	for <bio-software-list@hgmp.mrc.ac.uk>; Mon, 17 Jan 2000 19:11:25 GMT
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA29945
	for bio-software-list@hgmp.mrc.ac.uk; Mon, 17 Jan 2000 19:11:24 GMT
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: greg@franklin.burnham-inst.org (Dr. Greg Quinn)
X-Newsgroups: bionet.software
Subject: Re: Functional equivalent of GCG Findpatterns?
Date: 17 Jan 2000 19:16:23 GMT
Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE
Lines: 52
Message-ID: <85vpq7$1f1$1@franklin.ljcrf.edu>
References: <85r7gv$hso$1@franklin.ljcrf.edu> <sc4ogamrvj9.fsf@fes1.sanger.ac.uk> <sub3drw537m.fsf@europa.sanger.ac.uk>
X-Newsreader: TIN [UNIX 1.3 950824BETA PL0]
To: bio-software@hgmp.mrc.ac.uk
Sender: owner-bio-software@hgmp.mrc.ac.uk
Precedence: bulk

I appreciate the direction of the EMBOSS project,but I'm not sure that 
FuzzNuc, or I guess the one that I would be interested in, FuzzPro is 
the functional equivalent of FindPatterns; unless I missed something 
on the description page for FuzzPro, I didn't see a specific query
sequence syntax of the kind found in FindPatterns that precisely allows
me to specify particular residues at each position in the query. It's
this kind of ability which I'm looking for....

Peter Rice (pmr@sanger.ac.uk) wrote:
: Keith James <kdj@fes1.sanger.ac.uk> writes:
: 
: > >>>>> "Greg" == Greg Quinn <greg@franklin.burnham-inst.org> writes:
: > 
: >     Greg> Hi; Does anyone know of a publicly available functional
: >     Greg> equivalent of the GCG FindPatterns program?
: > 
: > The EMBOSS program fuzznuc will search sequences or databases for
: > arb