From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: "Petr Kuzmic" <pkuzmic@biokin.com>
Newsgroups: bionet.software
Subject: Program DYNAFIT updated
Date: 2 Dec 1998 05:15:09 GMT
Organization: BioKin Ltd.
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Version 3.14 of program DynaFit [P. Kuzmic (1996) Anal. Biochem. 237,
260-273] is available for download at http://www.biokin.com/dynafit/.

The program is useful for the statistical analysis of chemical kinetic,
enzyme kinetic, and receptor binding data.

__________________________________________________________
Petr Kuzmic * B i o K i n  Ltd. * http://www.biokin.com

From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: "tendo" <tendo@fas.harvard.edu>
Newsgroups: bionet.software
Subject: Re: FASTA format - proposed max line limit
Date: Wed, 2 Dec 1998 00:30:31 -0500
Organization: Harvard University, Cambridge, Massachusetts
Lines: 35
Message-ID: <742j7p$jgu$1@news.fas.harvard.edu>
References: <71qtgl$m8u@gap.cco.caltech.edu>    <72e3hu$p86$1@news.fas.harvard.edu> <72hpkf$hoi@gap.cco.caltech.edu>    <72hv4q$h09$1@news.fas.harvard.edu> <72op6t$2fh@news.u-strasbg.fr> <3650DB3D.84898F47@bioreason.com> <72qt83$i6o$1@news.fas.harvard.edu> <36542597.4145C085@bioreason.com> <731l4k$8lp$1@news.fas.harvard.edu> <73eok6$2oo@gap.cco.caltech.edu> <73mjou$tpm$1@news.fas.harvard.edu>
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I found that C++ standard template library (STL) allows you to access
unlimited length of string when you read a file.  So, as long as you use C++
as well as perl, the max line length limit is not necessary.

However, I still think it's a good idea to have secondary comment line which
is free from context....

Here's an example:

#include <cctype>
#include <string>

addseq(string& s, string& a) {
    for (long i=0; i<a.length(); a++)
        if (isalpha[i])
            s += a[i];
}

string readseq (istream& is) {
    string buffer;
    string seq;
    while (getline(is, buffer)) {
        if (buffer[0]=='>') {
            if (!seq.empty()) {
                something();
            }
            another();
        } else if (buffer[0] != ';')
            addseq(seq, buffer);
    }
}


toshi


From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar)
Newsgroups: bionet.software
Subject: Re: ClustalW problem
Date: 2 Dec 1998 04:43:42 GMT
Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison
Lines: 32
Sender: reguser@ebv.oncology.wisc.edu
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On Tue, 01 Dec 1998 18:01:30 -0800,
    Bernard P. Murray, PhD (bpmurray*STUFFER*@socrates.ucsf.edu) wrote:
>Hello there,

Hello Bernard -- First off thank you for sending me your program to
extract sequences from files created by Strider 1.2, and my apologies
for not responding in a more timely fashion.

>One strange thing I found was that when I tried to
>align two identical sequences (296 aa) with two somewhat scrambled but
>somewhat related fragments (eg. 100 aa) Clustal completely failed to
>spot the identical nature of the two long forms and "aligned" them in
>a very staggered manner.  

I could not reproduce this using clustalw-1.74 or 1.75 on my Linux
PC.  I used a file that had the following seven sequences:
1 & 4 = human hemoglobin beta chain
2 = horse hemoglobin beta chain
3 = human hemoglobin alpha chain
5 = sea-slug (Aplysia kurodai) myoglobin
6 = horse myoglobin
7 = human myoglobin

Perhaps you have encountered a Mac-specific bug in clustalw-1.74.  BTW,
have you tried this with clustalx?

Cheers,
Ashok
-- 
Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
aiyar@ebv.oncology.wisc.edu

From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: fibinachi@aol.comatose (Fibinachi)
Newsgroups: bionet.software
Subject: Re: hardware question
Lines: 8
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Date: 2 Dec 1998 04:16:53 GMT
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Message-ID: <19981201231653.26478.00000652@ng-ft1.aol.com>

I recently read an article about computers that use dna to solve complex
mathmatical problems.  I would like t know how one uses genetic code to solve
eqautions.
-==(UDIC)==-
Nights Mist Dragon
Http://www.geocities.com/athens/parthenon/6822
ICQ#14875814
"In life there are no innocents only the less guilty."

From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD)
Newsgroups: bionet.software
Subject: ClustalW problem
Date: Tue, 01 Dec 1998 18:01:30 -0800
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Lines: 29
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Hello there,

     I'm using ClustalW 1.74 for the Mac to compare protein database
sequences to weed out redundant/repeated occurrences.  I use the
default parameters and prepare the multiple sequence file in a
random order.  One strange thing I found was that when I tried to
align two identical sequences (296 aa) with two somewhat scrambled but
somewhat related fragments (eg. 100 aa) Clustal completely failed to
spot the identical nature of the two long forms and "aligned" them in
a very staggered manner.  I had thought that the initial clustering
was designed to stop these things happening.  Normally Clustal (since
version W) has behaved impeccably for me and happily aligns sequences
with big disparities in length (eg. a plasmid+insert sequence with
a small piece of the insert) so I was surprised to see this.
     Changing the order of the sequences in the file did not help.

Has anyone else come across this and how did you cope?
(ie. can you juggle the parameters or do you have to
perform pairwise alignments before constructing the multiple
sequence file?)

I'll test the same input file tonight with the DOS and Linux
versions just to make sure its not a Mac-specific effect.

     Curious,
          Bernard
-- 
Bernard P. Murray, PhD
Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA

From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: "SideshowBob" <kyhui@acs.ucalgary.ca>
Newsgroups: bionet.software
Subject: Re: hardware question
Date: Wed, 2 Dec 1998 08:30:12 -0700
Organization: The University of Calgary
Lines: 15
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I'm not sure what a DNA computer is, but maybe you're talking about Genetic
Algorithms?

Fibinachi wrote in message <19981130194715.03655.00000454@ng30.aol.com>...
>Exactly how does a DNA computer work?
>Please make it as simple as possible i got my degree in computer sciences
not
>biology.
>-==(UDIC)==-
>Nights Mist Dragon
>Http://www.geocities.com/athens/parthenon/6822
>ICQ#14875814
>"In life there are no innocents only the less guilty."



From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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Newsgroups: bionet.software
Subject: Free NetSpy permits to supervise the task on the remote PC.
From: fax_na@hotmail.com (A.E.)
Organization: private
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NetSpy permits to supervise the task on the remote PC.
It is useful tool for manager to see what the personnel is doing during the
work time.
NetSpy work in Win NT 4.x or Windows 95 (98) netowrk environment
using TCP/IP.

NetSpy consistes of 2parts  - server (NetSpyS) and client (Raposa).

The NetSpyS runs as minimized window. It is Gui application
Default TCP/IP port number is 79 for connection with client (Raposa).

(In demo version NetSpyS presents advetizing string read fron the host
UACT.NET. In this state NetSpyS is Always-on-top window)

It ispossible to use other port number,creating specila NetSpy.INI file and
put this file into the Windows directory. This file should have the following contents:

[Communication]
Port = 99

for port number 99 for example.

Client Raposa is console Windows application.
It should be started from virtual DOS (DOS-PROMT) by typing the following command
string:

>Raposa  network_remote_computer_name/IP__remote_computer [port_number]

By default the port number is 79 (Finger TCP/IP port - 79).

Port number should be the same as used by NetspyS.

Example of Raposa stating:

C:\WINNT40>raposa 127.0.0.1  99

or

C:\WINNT40>raposa ts1p12.uact.net

If connection was succesful the client Raposa would present the list
of tasks on the remote compute, for example:

E:\DOWN>a:\netspy\raposa 127.0.0.1  80

NetSpy Client Part. Questions: fax_na@hotmail.com
Connected to [127.0.0.1:80].

Conneted to the NetSpy Server
Host Name: gwork_a
The current date and time are: Fri Oct 16 20:15:20 1998

              Task Report

1.  Mimimized  NoZoomed Name: NetSpy Server Part
2.  NoMimimized  NoZoomed Name: NetDDE Agent
3.  NoMimimized  NoZoomed Name: Shortcut to cmd - a:\netspy\raposa 127.0.0.1  80

4.  NoMimimized  NoZoomed Name: Battery Meter
5.  NoMimimized  NoZoomed Name: OleMainThreadWndName
6.  NoMimimized  NoZoomed Name: Program Manager


Done!

E:\DOWN>

If you want to receive the sources of NetSpy or not-demo version 
(without demo string) please write to:
fax_na@hotmail.com












From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.wirehub.nl!oleane!jussieu.fr!cea.fr!not-for-mail
From: "MILOT Jean François" <Milot@cea.fr>
Newsgroups: bionet.software
Subject: phreeqc geochemical calculations
Date: 2 Dec 1998 12:08:00 GMT
Organization: SCD
Lines: 8
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is there anybody who knows a software called phreeqc which is a computer
program for speciation, reaction path, advective-transport, and inverse
geochemical calculations?
i need help !!!
thanks
(i'm french...)
seb
please e-mail me to : artous@amandine.cea.fr

From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: plxsrt@pln1.nott.ac.uk
Newsgroups: bionet.software
Subject: Re: FASTA format - proposed max line limit
Date: Wed, 02 Dec 1998 10:40:58 GMT
Organization: ACS, The University of Nottingham
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Sorry, this is slightly off the subject of the thread, but is there a
site where the details of the  common sequence file formats are
described in detail?  So if  changes are made  to a format such as
FASTA,  are these changes then  documented somewhere that is
publically accessible? 


Simon T


From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin)
Newsgroups: bionet.software
Subject: Re: ClustalW problem
Date: 2 Dec 1998 08:22:51 GMT
Organization: CRC - Universite Louis Pasteur - Strasbourg France
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    <slrn769hbf.4jb.aiyar@ebv.oncology.wisc.edu>
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In article <slrn769hbf.4jb.aiyar@ebv.oncology.wisc.edu>,
	aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) writes:

> Perhaps you have encountered a Mac-specific bug in clustalw-1.74.  BTW,
> have you tried this with clustalx?

	In fact it is the same algorithm, so it should give the same result.
	Using ClustalX would help finding the good matrix. In such a case, it
	is also usefull to log the process in a log file.

	If Bernard could send me both input and output file, I could have a
	look at what really happen in Clustal. The difference in length is a
	known problem that we are trying to work around, as described in the
	recent TiBS computer corner.

						François.
-- 
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France

From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: Peter Rice <pmr@sanger.ac.uk>
Newsgroups: bionet.software
Subject: Re: hardware question
Date: 02 Dec 1998 16:04:18 +0000
Organization: The Sanger Centre
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fibinachi@aol.comatose (Fibinachi) writes:

> I recently read an article about computers that use dna to solve complex
> mathmatical problems.  I would like t know how one uses genetic code to solve
> eqautions.

There was a paper a year or so ago in Science.

NP complete problems are tough for computers, but can be modelled by a
set of DNA sequences and reactions that explore all possibilities.

This gave rapid solutions to some problems, but could involve inpossibly
large quantities of DNA (several tons :-) for larger problems.

See:

      Science 1997 278: 446 
      Science 1994 266: 1021


-- 
----------------------------------------------------------------------
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-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: DEernisse@fullerton.edu (Doug Eernisse)
Newsgroups: bionet.software
Subject: Re: ClustalW problem
Date: Wed, 02 Dec 1998 14:49:39 -0800
Organization: CSUF
Lines: 57
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References: <bpmurray*STUFFER*-0112981801300001@mac-daddy.ucsf.edu>
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In article <bpmurray*STUFFER*-0112981801300001@mac-daddy.ucsf.edu>,
bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) wrote:

> Hello there,
> 
>      I'm using ClustalW 1.74 for the Mac to compare protein database
> sequences to weed out redundant/repeated occurrences.  I use the
> default parameters and prepare the multiple sequence file in a
> random order.  One strange thing I found was that when I tried to
> align two identical sequences (296 aa) with two somewhat scrambled but
> somewhat related fragments (eg. 100 aa) Clustal completely failed to
> spot the identical nature of the two long forms and "aligned" them in
> a very staggered manner.  I had thought that the initial clustering
> was designed to stop these things happening.  Normally Clustal (since
> version W) has behaved impeccably for me and happily aligns sequences
> with big disparities in length (eg. a plasmid+insert sequence with
> a small piece of the insert) so I was surprised to see this.
>      Changing the order of the sequences in the file did not help.
> 
> Has anyone else come across this and how did you cope?
> (ie. can you juggle the parameters or do you have to
> perform pairwise alignments before constructing the multiple
> sequence file?)
> 
> I'll test the same input file tonight with the DOS and Linux
> versions just to make sure its not a Mac-specific effect.
> 
>      Curious,
>           Bernard
> -- 
> Bernard P. Murray, PhD
> Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA

Not sure about the answer to your question, but perhaps you were
unaware of the newer interface for Clustal W called Clustal X.
It is much nicer to use, although the most current Mac PPC version seems
to be 1/98 (1.64) so perhaps your Clustal W is newer. See:

ftp://ftp.ebi.ac.uk/pub/software/mac/clustalw/clustalx/clustalx.hlp.html

ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalx 

ftp://ftp.ebi.ac.uk/pub/software/mac/clustalw/clustalx 

ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/clustalx 

Let us know when you figure out what is going on. That sounds odd.

Doug

-- 
Doug Eernisse
Department of Biological Science
California State University
Fullerton, CA 92834-6850 USA
<http://biology.fullerton.edu/people/faculty/doug-eernisse/>


From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: Gerard Tromp <tromp@sanger.med.wayne.edu>
Newsgroups: bionet.software
Subject: Re: hardware question
Date: Wed, 02 Dec 1998 11:04:52 -0500
Organization: Wayne State University
Lines: 27
Message-ID: <36656524.3914C2AC@sanger.med.wayne.edu>
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No, 
	it is not genetic algorithms. There was an experiment several years ago
using DNA to solve combinatorial problems such as the travelling
salesman problem (NP complete). I don't remember the details and vaguely
recall that it was discussed (if not reported in an article) in Science
at the time. It did appear to have promise although the implementation
was more than cumbersome.

SideshowBob wrote:
> 
> I'm not sure what a DNA computer is, but maybe you're talking about Genetic
> Algorithms?
> 
> Fibinachi wrote in message <19981130194715.03655.00000454@ng30.aol.com>...
> >Exactly how does a DNA computer work?
> >Please make it as simple as possible i got my degree in computer sciences
> not
> >biology.

Gerard
-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Gerard Tromp, Ph.D.
CMMG, Wayne State University    vox:	313-577-8773
3116, Scott Hall		fax: 	313-577-5218
540 E Canfield Ave		e-mail: tromp@sanger.med.wayne.edu
Detroit, MI 48201                       gtromp@cmb.biosci.wayne.edu

From owner-software@net.bio.net Tue Dec 01 22:00:00 1998
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From: "tendo" <tendo@fas.harvard.edu>
Newsgroups: bionet.software
Subject: Re: hardware question
Date: Tue, 1 Dec 1998 23:42:24 -0500
Organization: Harvard University, Cambridge, Massachusetts
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	charset="iso-2022-jp"
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>I recently read an article about computers that use dna to solve complex
>mathmatical problems.  I would like t know how one uses genetic code to
solve
>eqautions.


which article?  doesn't it explain anything?
actually I would like know what exactly it is, so why don't you ask the
author and explain us in *plain* English?

te


From owner-software@net.bio.net Wed Dec 02 22:00:00 1998
Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed1.earthlink.net!news-ana-24.sprintlink.net!news-west.sprintlink.net!news-stk-1.sprintlink.net!news-backup-west.sprintlink.net!news.sprintlink.net!itssrv1.ucsf.edu!macmac-2.ucsf.edu!user
From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD)
Newsgroups: bionet.software
Subject: Re: ClustalW problem
Date: Thu, 03 Dec 1998 13:14:23 -0700
Organization: University of California, San Francisco
Lines: 96
Message-ID: <bpmurray*STUFFER*-0312981314230001@macmac-2.ucsf.edu>
References: <bpmurray*STUFFER*-0112981801300001@mac-daddy.ucsf.edu> <slrn769hbf.4jb.aiyar@ebv.oncology.wisc.edu>
NNTP-Posting-Host: macmac-2.ucsf.edu

In a previous post I told you of a (Mac) ClustalW 1.74 problem
I encountered when aligning two identical sequences with two
fragments.  For those of you who are interested.  I'll summarise the
helpful suggestions and eventual solution to my problem.

It turned out that this was not a Mac-specific problem as
I could reproduce it with a variety of ClustalW versions
(1.6x and 1.7x) for DOS (DJGPP-compiled) and Linux (gcc).

Ashok Aiyar and Doug Ernisse suggested trying ClustalX
and, as I anticipated, I saw the same results with MacClustalX
and ClustalX for Win3.11.  My NCBI vibrant library is out of
date so I haven't compiled the Linux version with the
ClustalW 1.74 code but the 1.60 "engine" in ClustalX 1.3 for
Linux gave the same result.
     In fact, ClustalW should be the same as ClustalX as
Francois Jeanmougin one of the authors of the latter wrote...

In article <742tcr$due@news.u-strasbg.fr>, jeanmougin@igbmc.u-strasbg.fr wrote:

>         In fact it is the same algorithm, so it should give the same result.
>         Using ClustalX would help finding the good matrix. In such a case, it
>         is also usefull to log the process in a log file.
> 
>         If Bernard could send me both input and output file, I could have a
>         look at what really happen in Clustal. The difference in length is a
>         known problem that we are trying to work around, as described in the
>         recent TiBS computer corner.
> 
>                                                 François.

I have to admit that I have a problem with the different ClustalX
versions as they do not report which ClustalW "engine" they are
using.  I found ClustalX 1.3 uses ClustalW 1.6 etc.  You can only
work out what is happening by checking the source code.  I mainly
use ClustalW 1.74 as I haven't found a "ClustalX 1.74" or later.
This being said I am a great admirer of ClustalX, especially
of how portable it is.

THE CURE
========
The cure for the problem was given by in an e-mail from Julie Thompson
one of the authors of ClustalW 1.7 who advised me

>can I suggest that you try setting the 'Negative matrix' option
>in the multiple alignment parameters menu.

This solved the problem completely for all versions of ClustalW
and ClustalX.  However, it is necessary to either delete the old
.dnd guide file or specify a new filename or Clustal will insist
on using the old file with very strange results.

...and just to reply to the remainder of the posts...

In article <slrn769hbf.4jb.aiyar@ebv.oncology.wisc.edu>,
aiyar@aiyar.ml.org wrote:

> Hello Bernard -- First off thank you for sending me your program to
> extract sequences from files created by Strider 1.2, and my apologies
> for not responding in a more timely fashion.
..
> Cheers,
> Ashok

No worries.  I now have a Perl script (my first!) which should
do the same thing and is probably a little more flexible.
I can send you that as well if it will be useful.


     THANKS VERY MUCH to you all (especially Julie)

For the curious I include my ClustalW input file below.
This simply contains the four sequences retrieved when
looking for "heme oxygenase" and "chicken".  I used the
default parameters in Clustal.

>G123476:HO_CHICK:P14791
        1 metsqphnae smsqdlsell keatkevheq aentpfmknf qkgqvslhef klvtaslyfi
       61 ysaleeeier nkdnpvyapv yfpmelhrka alekdleyfy gsnwraeipc peatqkyver
      121 lhvvgkkhpe llvahaytry lgdlsggqvl kkiaqkalql pstgeglaff tfdgvsnatk
      181 fkqlyrsrmn alemdhatkk rvleeakkaf llniqvfeal qklvsksqen ghavqpkael
      241 rtrsvnkshe nspaagkese rtsrmqadml ttsplvrwll algfiattva vglfam
>G2735479:GGU95209:U95209
       1 metsqphnae smsqdlsell keatkevheq aentpfmknf qkgqvslhef k
>G104690:S09337
        1 nfqkgqvslx efklvtasly fiykaalekd leyfygsnwk hpellvahay tralqlpstg
       61 eglafftfdg vnatkfkqly vleeakkafl lniqvfealq klvsksq
>G104689:S15123
        1 metsqphnae smsqdlsell keatkevheq aentpfmknf qkgqvslhef klvtaslyfi
       61 ysaleeeier nkdnpvyapv yfpmelhrka alekdleyfy gsnwraeipc peatqkyver
      121 lhvvgkkhpe llvahaytry lgdlsggqvl kkiaqkalql pstgeglaff tfdgvsnatk
      181 fkqlyrsrmn alemdhatkk rvleeakkaf llniqvfeal qklvsksqen ghavqpkael
      241 rtrsvnkshe nspaagkese rtsrmqadml ttsplvrwll algfiattva vglfam
-- 
Bernard P. Murray, PhD
Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA

From owner-software@net.bio.net Wed Dec 02 22:00:00 1998
Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!nntp.flash.net!ihug.co.nz!not-for-mail
From: "John" <us168@usa.net>
Newsgroups: bionet.software
Subject: Software World
Date: 3 Dec 1998 22:45:06 GMT
Organization: The Internet Group Ltd
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Hi, my friends.

Please go to: http://members.tripod.com/~best_web/software.html
You can find a lot of useful software.


From owner-software@net.bio.net Thu Dec 03 22:00:00 1998
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From: "LUCAS" <lucassoft@hotmail.com>
Newsgroups: bionet.software
Subject: WINPROXY 2.2
Date: 4 Dec 1998 12:14:20 GMT
Organization: LUCASSOFT
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NNTP-Posting-Host: 194.65.176.129
X-Newsreader: Microsoft Internet News 4.70.1161

I would like to have a full version of winproxy 2.2 or higher.
Thanks


From owner-software@net.bio.net Thu Dec 03 22:00:00 1998
Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsfeed.cwix.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail
From: josephryan@yahoo.com
Newsgroups: bionet.software
Subject: Announce: NHGRI's WebBLAST 2.00.5 Beta1
Date: Fri, 04 Dec 1998 03:51:22 GMT
Organization: Deja News - The Leader in Internet Discussion
Lines: 110
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NHGRI's WebBLAST 2.00.5 Beta1
=====================

NHGRI's Computational Genomics Core is pleased to announce the first
Beta release of WebBLAST2.

Special Note
=====================

WebBLAST2 is software.  It runs on UNIX server and is used to organize,
analyze and annotate sequence data.  WebBLAST2 is not a public server
like NCBI's frontend to BLAST.

Download
=====================

WebBLAST2 is available for download from
    http://genome.nhgri.nih.gov/webblast/download/
While WebBLAST is in Beta, we require that you register before downloading.

Requirements
=====================

In order to install and use this package you will need Perl version
5.004 or better.  We recommend that you have the following packages
installed before you install WebBLAST:

1. NHGRI::Blastall.pm Version 0.22 or better
   ftp://ftp.nhgri.nih.gov/pub/software/blastall/

2. NCBI's local BLAST Version 2.0.6 or better
   ftp://ncbi.nlm.nih.gov/blast/executables/
   (for help installing NCBI's local BLAST see
    http://genome.nhgri.nih.gov/blastall/blast_install/)

3. SequenceUpload
   WebBLAST2 includes a MAC Droplet which is designed to simplify the process
   of transferring sequences to the Unix server from a Macintosh
   (connected to a sequencer).  This package is bundled separately.
    ftp://ftp.nhgri.nih.gov/pub/software/webblast/mac/

4. Staden (OPTIONAL)
   WebBLAST2 includes a Java Applet which allows one to examine Trace files.
   This Applet requires that Staden be installed on the same machine as the
   web server.  If you do not have Staden the TraceViewer will not work
   but everything else will.
   http://www.angis.org.au/Staden/

Changes
=====================

WebBLAST2 is a complete rewrite of WebBLAST1.  Changes in this version
include the dependancy on NCBI BLAST2 rather than NCBI BLAST1.
Much of the code has been encapsulated in the NHGRI::Blastall module
which allows for simpler bugfixes.  While WebBLAST1 used the auto-blast.plx
script for BLASTing only and used stat-blast.plx for parsing reports,
WebBLAST2 has combined both functionalities into auto-blast.plx.
WebBLAST2 includes support for multiple projects allowing for the
same binaries to support different sequencing efforts.  auto-blast.plx
allows for a project configuration file which allows for different
BLAST runs and cutoff criteria for different projects.  A Graphical
Viewer Applet has been added to the web display.   A TraceViewer,
developed at Whitehead Institute for Biomedical Research by Michael Zody,
has been added to the web display.  The Sequence Uploader has added support
for projects as well as display menus which allow for better more accurate
file transfer.

Support
=====================

Support is offered in the form of a mailing list.  Questions about how to
install and use WebBLAST should be directed to the web-blast-help mailing
list .  You can join the mailing list by sending a message to
majordomo@nhgri.nih.gov with the following command in the body of your
email message:

    subscribe webblast-help

More Info
=====================

There is more information available on the WebBLAST web site.

    http://genome.nhgri.nih.gov/webblast/

Public Domain Notice
=====================

This software/database is "United States Government Work" under the terms
of the United States Copyright Act. It was written as part of the authors'
official duties for the United States Government and thus cannot be
copyrighted. This software/database is freely available to the public for
use without a copyright notice. Restrictions cannot be placed on its present
or future use.

Although all reasonable efforts have been taken to ensure the accuracy
and reliability of the software and data, the National Human Genome
Research Institute (NHGRI) and the U.S. Government does not and cannot
warrant the performance or results that may be obtained by using this
software or data. NHGRI and the U.S. Government disclaims all warranties
as to performance, merchantability or fitness for any particular purpose.

In any work or product derived from this material, proper attribution
of the authors as the source of the software or data should be made, using
http://genome.nhgri.nih.gov/webblast as the citation.

Enjoy!

-----------== Posted via Deja News, The Discussion Network ==----------
http://www.dejanews.com/       Search, Read, Discuss, or Start Your Own    

From owner-software@net.bio.net Thu Dec 03 22:00:00 1998
Reply-To: "WCD80" <roddy@iname.com>
From: "WCD80" <roddy@iname.com>
Newsgroups: alt.comp.software.tools,bionet.software,comp.software,comp.software.international,comp.software-eng
References: <73eked$qa5@news.asiaonline.net>
Subject: Re: Any French OCR software?
Date: Fri, 4 Dec 1998 13:56:38 +0300
Lines: 21
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.0810.800
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.0810.800
Organization: Corbina ISP, http://www.corbina.net
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Cache-Post-Path: earth.corbina.net!unknown@roddy.dialup.corbina.ru
NNTP-Posting-Host: earth.corbina.net
X-Trace: 4 Dec 1998 14:00:42 +0300, earth.corbina.net
Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!newsfeed.gamma.ru!Gamma.RU!WWW1.relcom.ru!news.rosprint.net!earth.corbina.net!195.14.50.21

I have Finereader 4 and Cuniform98 with French support
For updated list of CDR progs and games
visit http://roddy.hypermart.net
Click Index
login : user
password: pass

Feel free to ask for not listed progs too !!!
If You receive CD with PASSWORD
get this utility http://roddy.hypermart.net/decrypt.zip

Kevin Cheng A. S. <kevin@minister.com> wrote in message
news:73eked$qa5@news.asiaonline.net...
>Is there any know any OCR software can recognize French in Windows 95?
>
>Kevin Cheng A. S.
>
>
>



From owner-software@net.bio.net Thu Dec 03 22:00:00 1998
Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!news.nottingham.ac.uk!not-for-mail
From: mbsrt@seqnet.dl.ac.uk (simon)
Newsgroups: bionet.software
Subject: Re: FASTA format - proposed max line limit
Date: Fri, 04 Dec 1998 10:52:48 GMT
Organization: ACS, The University of Nottingham
Lines: 23
Message-ID: <3667b97e.1231476@news.nott.ac.uk>
References: <71qtgl$m8u@gap.cco.caltech.edu> <71ssfa$rpp$1@flotsam.uits.indiana.edu> <7435fv$4tk$1@oyez.ccc.nottingham.ac.uk>
NNTP-Posting-Host: port41.ascend.ccc.nottingham.ac.uk
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>site where the details of the  common sequence file formats  and documented somewhere that is
>publically accessible? 
>
>Simon T
>
I suppose it's a sign of madness but in reply to my own post I know of
one such detailed collection of format information that comes with the
source for ReadSeq.  However, is there a more detailed collection
somewhere?

I don't know if anyone has mentioned this already but fasta format
files with long comments aren't much fun when you try to human-read
the file.   One of the reasons I like FASTA format is that it is
simple.   If you add a huge header line and you'll should surely have
no problem parsing the line [a line of any length could be computer
read by reading each character at a time until one equals the end of
line character- am I missing something here?] but you'll make it hard
work for the human eye trying to read the file. 

Simon T

    


From owner-software@net.bio.net Thu Dec 03 22:00:00 1998
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From: fibinachi@aol.comatose (Fibinachi)
Newsgroups: bionet.software
Subject: thanks for the help
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I  will read those articles
-==(UDIC)==-
Nights Mist Dragon
Http://www.geocities.com/athens/parthenon/6822
ICQ#14875814
"In life there are no innocents only the less guilty."

From owner-software@net.bio.net Thu Dec 03 22:00:00 1998
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From: amartin@stagleys.demon.co.uk (Andrew Martin)
Newsgroups: bionet.software
Subject: Re: FASTA format - proposed max line limit
Date: Thu, 3 Dec 1998 19:51:02 GMT
Organization: Private Address
Message-ID: <F3En53.4oD@stagleys.demon.co.uk>
References: <71qtgl$m8u@gap.cco.caltech.edu>    <72e3hu$p86$1@news.fas.harvard.edu> <72hpkf$hoi@gap.cco.caltech.edu>    <72hv4q$h09$1@news.fas.harvard.edu> <72op6t$2fh@news.u-strasbg.fr> <3650DB3D.84898F47@bioreason.com> <72qt83$i6o$1@news.fas.harvard.edu> <36542597.4145C085@bioreason.com> <731l4k$8lp$1@news.fas.harvard.edu> <73eok6$2oo@gap.cco.caltech.edu> <73mjou$tpm$1@news.fas.harvard.edu> <742j7p$jgu$1@news.fas.harvard.edu>
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tendo (tendo@fas.harvard.edu) wrote:
: I found that C++ standard template library (STL) allows you to access
: unlimited length of string when you read a file.  So, as long as you use C++
: as well as perl, the max line length limit is not necessary.

: However, I still think it's a good idea to have secondary comment line which
: is free from context....

I have a trivial C routine which replaces fgets() with fgetsany() to read
a line of any length.

EMail me if you want it!

Andrew

-------------------------------------------------------------------------
Dr. Andrew C.R. Martin
Lecturer in Biochemistry, UCL
-and- Technical Director, Inpharmatica Ltd.



From owner-software@net.bio.net Thu Dec 03 22:00:00 1998
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From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin)
Newsgroups: bionet.software
Subject: Re: ClustalW problem
Date: 4 Dec 1998 08:45:16 GMT
Organization: CRC - Universite Louis Pasteur - Strasbourg France
Lines: 55
Message-ID: <7487es$fiu@news.u-strasbg.fr>
References: <bpmurray*STUFFER*-0112981801300001@mac-daddy.ucsf.edu>
    <slrn769hbf.4jb.aiyar@ebv.oncology.wisc.edu>
    <bpmurray*STUFFER*-0312981314230001@macmac-2.ucsf.edu>
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In article <bpmurray*STUFFER*-0312981314230001@macmac-2.ucsf.edu>,
	bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) writes:

> I have to admit that I have a problem with the different ClustalX
> versions as they do not report which ClustalW "engine" they are
> using.  I found ClustalX 1.3 uses ClustalW 1.6 etc.  You can only
> work out what is happening by checking the source code.  I mainly
> use ClustalW 1.74 as I haven't found a "ClustalX 1.74" or later.

	Well, we though about that and here is the key. The latter number is
	the good one. So, because ClustalW is stable but ClustalX still
	depends of vibrant, clustalX stays beta.
	So, ClustalX 1.64b runs ClustalW 1.74. That's all. ClustalX 1.65b is a
	platform dependant bug correction (so that is why there is no 1.65b
	for all platforms).

	...

	Well, we have to clarify it a little bit more, probably for the 2.0
	version of Clustal (both X en W) :).

> This being said I am a great admirer of ClustalX, especially
> of how portable it is.

	Many thanks to all the users who report bugs or compiled it on so much
	different platform. Also, note that it is based on the vibrant
	interface (NCBI tool kit) and NCBI people helped us a lot in tracking
	platform dependant bugs.

> THE CURE
> ========
> The cure for the problem was given by in an e-mail from Julie Thompson

	That is a team work men ! :)))). Julie is always doing the code for
	both ClustalW and ClustalX and it stays a collaboration between all
	the authors of the ClustalX paper (and all the users).

> one of the authors of ClustalW 1.7 who advised me
> 
>>can I suggest that you try setting the 'Negative matrix' option
>>in the multiple alignment parameters menu.

	I advise everyone interested in Clustal problems and workaround to
	read the october computer corner in TiBS. The answer of you question
	was in it and probably other workarounds regarding several specific
	sets of sequences.

	And hopefully, such problem reports will help us improving the Clustal
	algorithm.

		Thanks to all!
						François.
-- 
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France

From owner-software@net.bio.net Thu Dec 03 22:00:00 1998
Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!SupernewsUK!supernews.com!SnNA!Supernews69!not-for-mail
From: "Pearce" <smithwip@ccmail.orst.edu>
Newsgroups: bionet.software,misc.forsale.computers.pc-specific.software,or.forsale,orst.forsale,us.forsale.computers
Subject: FS: Microsoft Software Titles
Date: Fri, 4 Dec 1998 12:53:04 -0800
Organization: Posted via Supernews, http://www.supernews.com - Discussions start here!
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X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2120.0

I have the following two Microsoft Software titles for sale:

MS Office Professional 97 (SBE)
MS Windows 95 (OSR2)

These are both on CD and OEM.  Being sold because I am switching to Linux.
I have original OEM documentation as well.

If you want them, email me with an offer at the following:

Home                                        Work
pearce72@usa.net                  smithwip@ccmail.orst.edu





From owner-software@net.bio.net Thu Dec 03 22:00:00 1998
Path: biosci!163.NET!fengbingjian
From: fengbingjian@163.NET (Feng Bingjian)
Newsgroups: bionet.software
Subject: (none)
Date: 4 Dec 1998 07:07:35 -0800
Organization: Home
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Hi
What is ClustalW and ClustalX, can they make alignment for gene sequences?
Is that for server or a PC?
If it can be run on a PC, where can i get it?
What is the most used algorithms for alignment?
thank you very much!
yours
Feng,Bingjian

fengbingjian@163.net


From owner-software@net.bio.net Fri Dec 04 22:00:00 1998
Path: biosci!EARTHLINK.NET!rjhayes1
From: rjhayes1@EARTHLINK.NET ("Robert Hayes")
Newsgroups: bionet.software
Subject: Software for dose-logit analysis
Date: 4 Dec 1998 19:57:41 -0800
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Can anyone recommend good software for dose-logit analysis?

Diane Stark, Ph.D.
dstark@xencor.com

Xencor Corporation
2585 Nina Street
Pasadena
CA 91107

Telephone: (626) 792-8608
Fax: (626) 792-4980

From owner-software@net.bio.net Fri Dec 04 22:00:00 1998
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From: mathog@seqaxp.bio.caltech.edu
Newsgroups: bionet.software
Subject: Re: FASTA format - proposed max line limit
Date: 5 Dec 1998 01:41:42 GMT
Organization: Biology Division, Caltech, Pasadena CA 91125
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In article <73mjou$tpm$1@news.fas.harvard.edu>, "tendo" <tendo@fas.harvard.edu> writes:
>There is a very good standard that only one comment line which starts with
>'>' character is allowed for each sequence.
>If lengths are really between 80-1000 chars, all you need is to just prepare
>1002 bytes buffer should be enough for reading or 2000 bytes for security.
>It's not a problem at all for any kind of recent computers, is it?

Yes, it is, but not in the sense you meant it.  The fundamental problem
with lines >80 characters is that there is no consistency in how they will
be displayed.  They might wrap, they might truncate, they might be scrolled
off the right hand side of the screen (which an end user might not notice
when scanning quickly through a 100 entry FASTA file with a tool like
"nedit" or "notepad").  There are even a few tools around which will do
nasty things when they encounter overly long "text" records, for instance
EDT on VMS will truncate them to 255 characters. 

>By my understanding, David's proposal is mainly focused on easy handling of
>FASTA fomrat data in programs and compatibility with available programs.

and consistency of display with a variety of tools.

FASTA is a TEXT format, so fasta files should look very much the same with
the widest range of existing text tools.  Long lines are not compatible 
with that goal.

Regards,

David Mathog
mathog@seqaxp.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech 

From owner-software@net.bio.net Fri Dec 04 22:00:00 1998
Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.u.washington.edu!learn
From: learn@u.washington.edu (Jerry Learn)
Newsgroups: bionet.software
Subject: Re: FASTA format - proposed max line limit
Date: Sat, 05 Dec 1998 11:59:01 -0800
Organization: University of Washington
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In article <74a30m$sjg@gap.cco.caltech.edu>, mathog@seqaxp.bio.caltech.edu
wrote:

> In article <73mjou$tpm$1@news.fas.harvard.edu>, "tendo"
<tendo@fas.harvard.edu> writes:
> >There is a very good standard that only one comment line which starts with
> >'>' character is allowed for each sequence.
> >If lengths are really between 80-1000 chars, all you need is to just prepare
> >1002 bytes buffer should be enough for reading or 2000 bytes for security.
> >It's not a problem at all for any kind of recent computers, is it?
> 
> Yes, it is, but not in the sense you meant it.  The fundamental problem
> with lines >80 characters is that there is no consistency in how they will
> be displayed.  They might wrap, they might truncate, they might be scrolled
> off the right hand side of the screen (which an end user might not notice
> when scanning quickly through a 100 entry FASTA file with a tool like
> "nedit" or "notepad").  There are even a few tools around which will do
> nasty things when they encounter overly long "text" records, for instance
> EDT on VMS will truncate them to 255 characters. 
> 
> >By my understanding, David's proposal is mainly focused on easy handling of
> >FASTA fomrat data in programs and compatibility with available programs.
> 
> and consistency of display with a variety of tools.
> 
> FASTA is a TEXT format, so fasta files should look very much the same with
> the widest range of existing text tools.  Long lines are not compatible 
> with that goal.
> 
One other benefit with constraining the comment line to 80 characters is
that the sequence files are e-mailable. Often I ask collaborators to send
me sequence data via email. It is usually the most convenient LCD method
to exchange data. If the comment line is >80 characters, the remaining
characters become sequence data.

Jerry Learn

From owner-software@net.bio.net Fri Dec 04 22:00:00 1998
Path: biosci!NET.BIO.NET!kristoff
From: kristoff@NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.software
Subject: Performance of Linux systems for BLAST searching??
Date: 4 Dec 1998 19:48:14 -0800
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I'm thinking about setting up an in-house BLAST server on a limited
budget and was wondering what kind of performance people are getting
out of Linux machines these days.  I've received some attractive
quotes on 600 MHz Alpha and dual 450 MHz Pentium II systems with 1 GB
of RAM in the $6,000 - $8,000 range.  I'd be interested in hearing
people's experiences with similar systems.

Sincerely,

Dave Kristofferson
ex-BIOSCI/bionet Manager
kristoff@net.bio.net


From owner-software@net.bio.net Sat Dec 05 22:00:00 1998
Message-ID: <366A2684.A65028EE@bioreason.com>
Date: Sat, 05 Dec 1998 22:39:00 -0800
From: Andrew Dalke <dalke@bioreason.com>
Organization: Bioreason, Inc.
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Subject: Re: FASTA format - proposed max line limit
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David Mathog <mathog@seqaxp.bio.caltech.edu> said:
> Yes, it is, but not in the sense you meant it.  The fundamental problem
> with lines >80 characters is that there is no consistency in how they
> will be displayed.  They might wrap, they might truncate, they might be
> scrolled off the right hand side of the screen (which an end user might
> not notice when scanning quickly through a 100 entry FASTA file with a
> tool like "nedit" or "notepad").  There are even a few tools around
> which will do nasty things when they encounter overly long "text"
> records, for instance EDT on VMS will truncate them to 255 characters. 

I'll argue that they're using the wrong tools or not using their tools
well enough.  There exist solutions for all those platforms (well, I'm
not sure about VMS but you can probably get emacs for it).

  NEdit will let you choose several wrap styles under "Preferences-Wrap"
There's None, Auto Newline, Continuous (you probably want the last one).
You could probably define a macro to go into the right mode by default
when a .fasta file is read.
  
  Notepad is I understand a lousy text viewer.  One recommendation I've
heard is at http://x6.dejanews.com/getdoc.xp?
AN=414147166&CONTEXT=912925389.2082734198&hitnum=2
which suggests getting the free NoteTab Light from
http://www.notetab.com/ .  It even has a menu option to replace or
reinstall Notepad as the default viewer.  I don't have a MS machine
so I cannot tell how it deals with word wraps.  What description is
online is that it can do a lot.

  I'll bet BBEdit for the Mac handles line wrapping issues easily
  as well.

  Or, put it another way.  Suppose you're looking at a structure
file.  Do you want to look at the 2D/3D coordinates in a text editor
(after all, they are text files) or in a structure viewer?  FASTA
happens to contain simple enough data that a basic text viewer
usually works well, but it doesn't always work.  Given that more
advanced, free, powerful, easier and in some cases fully backwards
compatible tools exist, why worry about stunting an existing format
(and breaking compatibility with other software).


> FASTA is a TEXT format, so fasta files should look very much the
> same with the widest range of existing text tools.  Long lines are
> not compatible with that goal.

  Just because something is in text, or more specifically ASCII (since
Unicode is text) doesn't mean it is designed to be human readable.
Here's a couple of counter-examples, from an interactive Python
session:

>>> print pickle.dumps( ("This is a comment", "EKLADWERDNA") )
(S'This is a comment'
p0
S'EKLADWERDNA'
p1
tp2
.
>>> infile = StringIO.StringIO(">This is a comment\nEKLADWERDNA\n")
>>> uu.encode(infile, sys.stdout)
begin 666 -
?/E1H:7,@:7,@82!C;VUM96YT"D5+3$%$5T521$Y!"@  
 
end

Both of these are TEXT representations, but the first is designed to
store complex data structures in an form easily parsable for a
computer and somewhat parsable for a human (so says the format
documentation) while the second is designed to send any text data via
email/usenet to software designed for limited text displays.  In the
case of uuencode/uudecode, the text width is about 61 characters as
many older terminals had 65 character displays.  Be thankful we can
expect 80 these days :)


  I persist in saying that the FASTA file is poorly designed and
overused.  It's 90% good enough, and simple, so it has become the de
facto sequence format.  It's the other 10% that makes it nasty,
like not expecting people would overload the single line comment
information and so forcing long lines which make it less readable.

  To stay in the strictures of the existing format, your proposal is
to limit the format even more by keeping the line width under 80
characters.  As I pointed out in an earlier email, there is existing
software that expects it can put more than 80 characters in a line. 
If you're going to change the format to make existing software
unusable, why not remove restrictions instead of adding new ones?

  Here's a format that I'll call FASTA-Next Generation (in homage to
IP-NG which was in homage to Star Trek, Next Generation :).  The
extension for this format is ".fng" and the MIME type is
chemical/fasta-ng.  It should make a FASTA variant that's 95% good
enough, and as good as I think you can do and still be FASTA-like.

  All this format does is extend the existing FASTA format by allowing
multiple successive comment lines.  Instead of having one long line,
that line can be folded across many lines.

Here's a more formal definition in BNF:

  FNG_FILE ::=
       NEWLINE*
     | BLANK* RECORD+
     ;

  NEWLINE ::=  "\r\n";

  RECORD ::=  COMMENT+ SEQUENCE+ NEWLINE*;

  COMMENT ::= '>' text+  NEWLINE;

  SEQUENCE ::= text+ NEWLINE;

The definition of "text" is given by RFC 822, Appendix D (see
http://info.internet.isi.edu:80/in-notes/rfc/files/rfc822.txt) as:
text        =  <any CHAR, including bare CR & bare LF, but NOT
                including CRLF>
CHAR        =  <any ASCII character>  ; (  octal 0-177,  decimal 0-127)
CR          =  <ASCII CR, carriage return>  ; ( octal 15, decimal 13)
CRLF        =  CR LF
LF          =  <ASCII LF, linefeed>         ; ( octal 12, decimal 10)

My format proposal requires that lines end with CRLF, also as suggested
in the RFC.

It is urged that implementers of FNG parsers offer an option to
recognize ASCII CR (Macs) and ASCII LF (Unix) as alternate newline
characters to support noncompliant implementations.  The option should
not be enabled by default because of the definition of CHAR given
above.  It is also urged that writers of FNG files do not use CR or LF
other than as CRLF because of these portability issues.

For readability, long text in the comment and sequence fields
> may be "folded" onto multiple lines of the actual field.
>
> "Long" is commonly interpreted to mean greater than 65 or 72
> characters.  The former length serves as a limit, when the message
> is to be viewed on most simple terminals which use simple display
> software; however, the limit is not imposed by this standard.
> 
>    Note:  Some display software often can selectively fold lines,
>           to  suit  the display terminal.  In such cases, sender-
>           provided  folding  can  interfere  with   the   display
>           software.
                               -- RFC 822, section 3.4.8

It is strongly urged that users of this format not place complex
information inside of the comment section.  Other formats, such as
XML, are more appropriate.  Whitespace should only be used in the
comment section to indicate seperations between words and must not
be used to align information between multiple lines (that is,
whitespace must not be used for vertical alignment).  No implicit
whitespace is assumed by a CRLF.

In other words, the following comment lines
>This is a
> comm
>ent line.

is semantically equivalent to "This is a comment line."  (There is no
whitespace at the end of any of the three lines.)


There should be a paragraph here saying that (I think) whitespace is
important inside of the sequence section and that tabs and spaces are
not interconvertable.  I don't know enought about the use of spaces as
a gap character to know how to write this.  In this case, CRLF should
still not act as any sort of whitespace.


  This proposal is:
   o well-defined
   o cross platform
   o a superset of the existing FASTA format (excepting newline
       conversion)
   o easy to parse
   o a "normal looking" extension of common usage
   o great for MS Windows users since that OS uses CRLF as the system
      default newline.

Because the comment and sequence fields can be folded across multiple
lines without loosing any semantic meaning, it is also possible to
convert any FNG file to a FNG file that uses less than 80 characters
per line.  Conversion of such a folded file to a "classic FASTA"
format is trivial; remove CRLF used between comment lines in the
same record.  If a program doesn't support "long" lines the input
can be filtered with no loss of information.  Or the output can
be filtered to normalize to the in-house standards.

Also, excepting the newline issue and some whitespace details, there's
already software that understands this format since it's a natural
extension of the existing format.

There's other things I would like, including format version
information, but to stay close the existing FASTA format I'll hold
back.


Any comments?  Any reason this format is inappropriate for those
places where the current FASTA file is appropriate?  Any problems with
it?  Remember, suggestions that changes current practices (like
limiting line length) is incompatable with existing software, so why
not make things better instead of worse?

						Andrew Dalke
						dalke@bioreason.com

From owner-software@net.bio.net Sat Dec 05 22:00:00 1998
Message-ID: <366A2689.AAD5B4AE@bioreason.com>
Date: Sat, 05 Dec 1998 22:39:05 -0800
From: Andrew Dalke <dalke@bioreason.com>
Organization: Bioreason, Inc.
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Subject: Re: FASTA format - proposed max line limit
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Jerry Learn <learn@u.washington.edu> commented:
> One other benefit with constraining the comment line to 80 characters is
> that the sequence files are e-mailable. Often I ask collaborators to send
> me sequence data via email. It is usually the most convenient LCD method
> to exchange data. If the comment line is >80 characters, the remaining
> characters become sequence data.

That's why there are MIME attachments.  Most modern mailers (the
formal MIME definition started with RFC 1341 in 1992) let you attach
files to your email.  Many cheap or even free email clients exist
to handle this sort of mail, ranging from Eudora to Netscape to
PINE, ELM and Mutt.  There's no reason to expect that a "least common
denominator" approach cannot take advantage of that.


Even before MIME you could still send uuencoded mail.  In the good old
days I sent lots of mail like:
 cat /etc/passwd | compress | uuencode passwd.Z | Mail dalke@acm.org
(Let's see who tries that out :)

That's how people sent (and still send) images on Usenet.  Most capable
news readers can automatically decode those mailings even when sent
as several posts.  (Sent as several posts because another limitation
of mail/usenet is a hard limit by some gateways on message size.
And there's no way a format will get around that limitation.)

Also, do you know what sorts of mangling occur for email to get
to you.  You mentioned forcing line wraps (even though the SMTP
RFC says mailer should allow long lines) but do you know about the
"From " problem?  Take a look at:

  http://www.tamos.net/guide/manpages/qmail/mbox.5.html

The "mbox" mailbox format uses a line that starts "From " to indicate
the start of a new email message.  If text in the body starts with
"From ", the local mail delivery agent (the program that puts the
new email in the file) is supposed to escape the "From " with
">From ".  The mail reader is then supposed to unescape it so
you never see the leading ">".  However, the original format did
not escape escaped test (eg, convert ">From" to ">>From", ">>From"
to ">>>From", etc.)

Quoting from the above url (and with a different quote character :)
| The original mboxo format quotes  only  From_  lines,  not
| >From_  lines.   As  a  result  it  is  impossible to tell
|  whether
|
|        From: djb@silverton.berkeley.edu (D. J. Bernstein)
|        To: god@heaven.af.mil
|
|        >From now through August I'll be doing beta  testing.
|        Thanks for your interest.
|
|  was quoted in the original message.

Before you object, I do get email that is escaped this way;
where I see the additional ">" in the front of mail body lines
starting with "From ".

In fact, let's try it out :)
From 0
>From 1
>>From 2
>>>From 3

Of course, Usenet posts do things different than email, so the
only ones that might be bothered by this are people who read
posts stored as email files (old pine users) and those reading
this group from a news->email gateway.

So suppose the FASTA sequence sent to you were:
| >This is from E.coli
| AAAAAAAAA
| >From yeast
| TTTTTTTT

it is quite possible for you to see the email as
| >This is from E.coli
| AAAAAAAAA
| From yeast
| TTTTTTTT

which if you copied and pasted would be interpreted as

| >This is from E.coli
| AAAAAAAAAFrom yeastTTTTTTTT

If the software you're using skips characters it doesn't recognize,
you wouldn't even notice.

In some sense, by arguing that the line limit must be < 80 columns
because of mail concerns, you also argue the format should never
contain ">From " at the start of a comment line.

In closing, use MIME.  It's good for you. :)

						Andrew Dalke
						dalke@bioreason.com

From owner-software@net.bio.net Sat Dec 05 22:00:00 1998
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Subject: Sindacato Autonomo Informatici
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SINDACATO AUTONOMO INFORMATICI



Come tutti sappiamo i lavoratori informatici sono da sempre integrati come
impiegati in ogni tipo di contratto nazionale, ne risulta che poche persone
in ambiti maggiori abbiano problematiche molto diverse da quelle dei
colleghi dello stesso contratto.

Un esempio lampante è costituito dalle software-house che aderiscono o
aderivano, per motivi fiscali, quasi tutti al contratto Metalmeccanico.

Il discorso non e’ diverso se si prendono in considerazione le grosse realtà
produttive italiane; le aziende assicurative, industriali, commerciali, e
bancarie, dispongono di un ristretto numero di persone che hanno mansioni d’
estrema responsabilità sia di riservatezza sia funzionali/organizzative.

Il risultato è che la logica del tesseramento alle organizzazioni sindacali
non consente una soddisfacente tutela di questi lavoratori chiamati spesso
dal datore di lavoro a superlavoro o peggio ancora a funzione di parafulmine
di decisioni avventate prese in ambiti più elevati.

Quali interessi possono avere le organizzazioni sindacali nel tutelare una
ristrettissima percentuale di lavoratori (tesserati) che invece possono
essere, molto spesso merce di scambio, vedi la facilità che avvenga dello
straordinario eccessivo e, aggiungo, non permesso in altre mansioni, con il
datore di lavoro per contratti integrativi a tutto vantaggio della maggior
parte dei suoi tesserati.

Per i lavoratori informatici queste non sono affatto novità ma mi domando
perché non si pensa di raccogliere le forze e far pesare nel giusto modo l’
enorme potere contrattuale che è in grado di sostenere una parte molto
importante, benché non interessante numericamente, dei lavoratori dell’
intero processo produttivo italiano.

Ho intenzione di raccogliere per Voi adesioni e, se si raggiungeranno numeri
interessanti, cercare di far riconoscere a Roma il nuovo sindacato affinché
questa corsa al liberismo non schiacci ancora di più quella categoria,
ristretta, di lavoratori che fino adesso hanno dato una grossa spinta alla
ripresa italiana con la loro professionalità e disponibilità e che meritano
una maggior considerazione.




From owner-software@net.bio.net Sat Dec 05 22:00:00 1998
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From: Rich Teresi <Teresi@apk.net>
Newsgroups: bionet.software
Subject: No subject was specified.
Date: Sun, 06 Dec 1998 11:13:05 +0000
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subscribe  Rich Teresi


From owner-software@net.bio.net Sat Dec 05 22:00:00 1998
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From: "S.W. Rasmussen" <swr@crc.dk>
Newsgroups: bionet.software
Subject: Dnatools, sequence software
Date: Mon, 07 Dec 1998 00:25:50 +0100
Organization: Carlsberg Laboratory
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DNATools is a program package for handling and analysis of DNA and
protein
sequences. It includes a number of general facilities for sequence
editing, restriction enzyme mapping, translation into protein etc. but
also several more complex functions for creation of codon tables, primer
design and ordering, SAGE analysis, etc.

Visit our home page at:

http://www.crc.dk/phys/A01B04_dnatools.htm

Dr. Søren W. Rasmussen
Carlsberg Laboratory
Dept. of Physiology
Copenhagen, Denmark
http://www.crc.dk/phys/index.htm


From owner-software@net.bio.net Sat Dec 05 22:00:00 1998
Path: biosci!news.stanford.edu!logbridge.uoregon.edu!netnews1.nw.verio.net!netnews.nwnet.net!news.u.washington.edu!learn
From: learn@u.washington.edu (Jerry Learn)
Newsgroups: bionet.software
Subject: Re: FASTA format - proposed max line limit
Date: Sun, 06 Dec 1998 08:07:46 -0800
Organization: University of Washington
Lines: 42
Message-ID: <learn-0612980807460001@cs107-13.u.washington.edu>
References: <71qtgl$m8u@gap.cco.caltech.edu> <72e3hu$p86$1@news.fas.harvard.edu> <72hpkf$hoi@gap.cco.caltech.edu> <72hv4q$h09$1@news.fas.harvard.edu> <72op6t$2fh@news.u-strasbg.fr> <3650DB3D.84898F47@bioreason.com> <72qt83$i6o$1@news.fas.harvard.edu> <36542597.4145C085@bioreason.com> <731l4k$8lp$1@news.fas.harvard.edu> <73eok6$2oo@gap.cco.caltech.edu> <74a30m$sjg@gap.cco.caltech.edu> <learn-0512981159010001@cs114-3.u.washington.edu> <366A2689.AAD5B4AE@bioreason.com>
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        UVsx&b~@,Bcu

In article <366A2689.AAD5B4AE@bioreason.com>, Andrew Dalke
<dalke@bioreason.com> wrote:

> Jerry Learn <learn@u.washington.edu> commented:
> > One other benefit with constraining the comment line to 80 characters is
> > that the sequence files are e-mailable. Often I ask collaborators to send
> > me sequence data via email. It is usually the most convenient LCD method
> > to exchange data. If the comment line is >80 characters, the remaining
> > characters become sequence data.
> 
> That's why there are MIME attachments.  Most modern mailers (the
> formal MIME definition started with RFC 1341 in 1992) let you attach
> files to your email.  Many cheap or even free email clients exist
> to handle this sort of mail, ranging from Eudora to Netscape to
> PINE, ELM and Mutt.  There's no reason to expect that a "least common
> denominator" approach cannot take advantage of that.
> 

<tutorial omitted>

> 
> In closing, use MIME.  It's good for you. :)
> 
>                                                 Andrew Dalke
>                                                 dalke@bioreason.com

Andrew,

I'm glad I provided you with an opportunity to tell us all about MIME and
email. 

Of course, I already know about mime attachments and use them quite often.
My collaborators very quite a bit in their email-savvy, and I would prefer
no to have to provide them with instructions on how to use there email
program. Instead, I ask them to send the file as an attachment and if they
can't do that to send the file as an email message. 

If they want to name their sequences using "From yeast" and "From E.
coli," then I ahve to hav a different discussion on how to name one's
sequences.

Jerry

From owner-software@net.bio.net Sat Dec 05 22:00:00 1998
Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!Supernews60!supernews.com!gestalt!shiva.direcpc.com!not-for-mail
From: "CCT" <cct@mail.direcpc.com>
Newsgroups: bionet.software
Subject: MS Office 97 Pro - MS Win NT 4.0 Workstation
Date: Sat, 5 Dec 1998 21:56:13 -0500
Organization: DirecPC
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Message-ID: <74cs00$mmk$3@shiva.direcpc.com>
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X-Priority: 3
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X-Newsreader: Microsoft Outlook Express 5.00.0810.800
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.0810.800

We carry MS Office 97 Pro on CD with license, registration certificate and
manual for only $169.00.  Win NT 4.0 workstation for only $130.00

http://www.cct-computers.com





From owner-software@net.bio.net Sun Dec 06 22:00:00 1998
Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!news-lond.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!jussieu.fr!univ-angers.fr!ciril.fr!u-strasbg.fr!news
From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin)
Newsgroups: bionet.software
Subject: Clustal (was Re: (none))
Date: 7 Dec 1998 12:09:03 GMT
Organization: CRC - Universite Louis Pasteur - Strasbourg France
Lines: 33
Message-ID: <74gggv$6n0@news.u-strasbg.fr>
References: <199812041507.HAA07487@net.bio.net>
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In article <199812041507.HAA07487@net.bio.net>,
	fengbingjian@163.NET (Feng Bingjian) writes:
> Hi
> What is ClustalW and ClustalX, can they make alignment for gene sequences?

	ClustalW is a multiple alignment program. clustalX is its
	multi-platform grafic user interface.

	what do you mean "gene sequences"? It is NOT a fragment assembly
	program. The Staden package provide a fragment assembly program. It
	can be sused to align DNA sequences.

> Is that for server or a PC?

	It can run and mostly all unices, Mac, and Windows 32bits platforms.

> If it can be run on a PC, where can i get it?

	ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/

> What is the most used algorithms for alignment?

	Probably, you can try to get the last Trends in Genetics or read the
book "Methods in enzymology". You will probably have all the answers in it.

> thank you very much!

	Pleased. But next time, add a subject to your post. It might help.

						François.
-- 
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France

From owner-software@net.bio.net Sun Dec 06 22:00:00 1998
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From: amartin@stagleys.demon.co.uk (Andrew Martin)
Newsgroups: bionet.software
Subject: Re: Performance of Linux systems for BLAST searching??
Date: Mon, 7 Dec 1998 00:08:42 GMT
Organization: Private Address
Message-ID: <F3KJ2I.ACp@stagleys.demon.co.uk>
References: <CMM-RU.1.4.912829690.kristoff@net.bio.net>
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Dave Kristofferson (kristoff@NET.BIO.NET) wrote:

: I'm thinking about setting up an in-house BLAST server on a limited
: budget and was wondering what kind of performance people are getting
: out of Linux machines these days.  I've received some attractive
: quotes on 600 MHz Alpha and dual 450 MHz Pentium II systems with 1 GB
: of RAM in the $6,000 - $8,000 range.  I'd be interested in hearing
: people's experiences with similar systems.

: Sincerely,

: Dave Kristofferson

Alpha works great if you compile using DEC CC under Digital Unix then use the
executable. Not so good complied with GCC under Linux. About 30% slower
for a start. Also there seem to be some probs. with the maths libraries
and PSI-BLAST as opposed to BLAST crashes randomly. (BLAST also crashes,
but there is a fairly straightforward fix (one of the maths calls
causes a numeric underflow in calculating E from the bit-score).

Hope that helps,

Andrew



From owner-software@net.bio.net Sun Dec 06 22:00:00 1998
Message-ID: <366C00A4.EB036D32@bioreason.com>
Date: Mon, 07 Dec 1998 08:21:56 -0800
From: Andrew Dalke <dalke@bioreason.com>
Organization: Bioreason, Inc.
X-Mailer: Mozilla 4.05 [en] (X11; U; IRIX 6.2 IP22)
MIME-Version: 1.0
Newsgroups: bionet.software
Subject: Re: FASTA format - proposed max line limit
References: <71qtgl$m8u@gap.cco.caltech.edu> <72e3hu$p86$1@news.fas.harvard.edu> <72hpkf$hoi@gap.cco.caltech.edu> <72hv4q$h09$1@news.fas.harvard.edu> <72op6t$2fh@news.u-strasbg.fr> <3650DB3D.84898F47@bioreason.com> <72qt83$i6o$1@news.fas.harvard.edu> <36542597.4145C085@bioreason.com> <731l4k$8lp$1@news.fas.harvard.edu> <73eok6$2oo@gap.cco.caltech.edu> <74a30m$sjg@gap.cco.caltech.edu> <learn-0512981159010001@cs114-3.u.washington.edu> <366A2689.AAD5B4AE@bioreason.com> <learn-0612980807460001@cs107-13.u.washington.edu>
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Jerry Learn <learn@u.washington.edu> said:
> I'm glad I provided you with an opportunity to tell us all about
> MIME and email. 

  I apologize.  I had a tendency to write email that's too
tutorial-like.  I meant no slur on your or anyone else's knowledge
of email.


  The point of my response was to say that the criterion for
a file format should not be determined by the limitations of
non-MIME based email.  In addition to the display problems
presented by some email clients there are hidden dangers present
in standard email.  One of them is the ">From" issue I pointed out.
These are not well known but have consequences on sending files as
raw email text.  There may be other considerations I don't know
about, esp. as regards non-unix mailers.

> If they want to name their sequences using "From yeast" and
> "From E. coli," then I ahve to hav a different discussion on
> how to name one's sequences.

  That choice of names was for example purposes only.  There's 
no reason that something similar isn't going to happen.  For example,
consider a program that merges multiple sequence records as the
following:

 >sp|0001
 AAAA
 >gb|0002 
 AAAA
 >sp|0009

merged into
 >From sp|0001, gb|0002 and sp|0009
 AAAA

In this case the author decided to make the comments of the merged
record more human readable.

						Andrew Dalke
						dalke@bioreason.com

From owner-software@net.bio.net Sun Dec 06 22:00:00 1998
Path: biosci!biosci!not-for-mail
From: Ewan Birney <birney@sanger.ac.uk>
Newsgroups: bionet.software
Subject: Pfam release 3.3
Date: 7 Dec 1998 11:31:41 -0800
Organization: MRC Human Genome Mapping Project Resource Centre
Lines: 40
Sender: daemon@net.bio.net
Distribution: world
Message-ID: <Pine.OSF.4.00.9812071731080.22981-100000@scarp.sanger.ac.uk>
NNTP-Posting-Host: net.bio.net



                ANNOUNCING PFAM RELEASE 3.3
                ===========================

Pfam is a collection of protein domain family alignments which were
constructed semi-automatically using profile hidden Markov models.
Pfam families contain functional annotation and cross-references to
other databases.  Query sequences can be searched against the Pfam
library of profile hidden Markov models at the web sites below.

Pfam 3.3 contains 1390 families.  57% of proteins in SWISSPROT 35
and TrEMBL 5 have at least one match to a Pfam family.

The changes between Pfam release 3.3 and Pfam release 3.2 are:

         46 new families have been added.

For interactive access and searching see URLs

               http://www.sanger.ac.uk/Software/Pfam/
               http://pfam.wustl.edu/
               http://www.cgr.ki.se/Pfam/

The release is also available in flat file by anonymous ftp:

               ftp://ftp.sanger.ac.uk/pub/databases/Pfam/
               ftp://ftp.genetics.wustl.edu/pub/Pfam/

The Pfam HMM library is compatible with HMMER2 software, available
from
	       http://hmmer.wustl.edu/


___________________
The Pfam consortium
December 1998




From owner-software@net.bio.net Sun Dec 06 22:00:00 1998
Message-ID: <366C2E36.F4369996@bioreason.com>
Date: Mon, 07 Dec 1998 11:36:22 -0800
From: Andrew Dalke <dalke@bioreason.com>
Organization: Bioreason, Inc.
X-Mailer: Mozilla 4.05 [en] (X11; U; IRIX 6.2 IP22)
MIME-Version: 1.0
Newsgroups: bionet.software
Subject: Re: FASTA format - proposed max line limit
References: <71qtgl$m8u@gap.cco.caltech.edu> <72e3hu$p86$1@news.fas.harvard.edu> <72hpkf$hoi@gap.cco.caltech.edu> <72hv4q$h09$1@news.fas.harvard.edu> <72op6t$2fh@news.u-strasbg.fr> <3650DB3D.84898F47@bioreason.com> <72qt83$i6o$1@news.fas.harvard.edu> <36542597.4145C085@bioreason.com> <731l4k$8lp$1@news.fas.harvard.edu> <73eok6$2oo@gap.cco.caltech.edu> <74a30m$sjg@gap.cco.caltech.edu> <learn-0512981159010001@cs114-3.u.washington.edu> <366A2689.AAD5B4AE@bioreason.com> <learn-0612980807460001@cs107-13.u.washington.edu> <366C00A4.EB036D32@bioreason.com>
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Ooops, a couple omissions in that last post (concerning effects of
email on sequence file formats).

 >sp|0009

should be
 >sp|0009
 AAAA

and
> In this case the author decided to make the comments of the merged
> record more human readable.

should be
> In this case the author ***of the software which merges sequence
> entries*** decided to make ...

to distinguish from the author of the post to which I was replying.

						Andrew Dalke
						dalke@bioreason.com

From owner-software@net.bio.net Sun Dec 06 22:00:00 1998
Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.cwix.com!204.210.0.20!news.san.rr.com!nntp3.cerf.net!news.ycc.yale.edu!not-for-mail
From: Joerg Daehn <jdaehn@stud.uni-hannover.de>
Newsgroups: bionet.software
Subject: Looking for unix program converting medline to bibtex
Date: Mon, 07 Dec 1998 13:13:29 -0400
Organization: Yale University
Lines: 14
Message-ID: <366C0CB6.BF58475B@stud.uni-hannover.de>
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Hi,

some weeks ago I came across a Webpage for a unix-based, x11-gui program
which converted medline outputs and others to diverse bibliography
formats (endnote, bibtex). But unfortunately I didn't bookmark that
page. Now I can't find it anymore. As I am about to write my thesis and
wanted to start this week I am a little desperate. Does anybody know
about a tool like that and it's location on the web? It is supposed to
be freeware, in beta status and made by a french instiitute/university.

Thanx

Joerg


From owner-software@net.bio.net Sun Dec 06 22:00:00 1998
Message-ID: <366C0363.A4C9CBAF@bioreason.com>
Date: Mon, 07 Dec 1998 08:33:39 -0800
From: Andrew Dalke <dalke@bioreason.com>
Organization: Bioreason, Inc.
X-Mailer: Mozilla 4.05 [en] (X11; U; IRIX 6.2 IP22)
MIME-Version: 1.0
Newsgroups: bionet.software
Subject: Re: Performance of Linux systems for BLAST searching??
References: <CMM-RU.1.4.912829690.kristoff@net.bio.net> <F3KJ2I.ACp@stagleys.demon.co.uk>
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Andrew Martin <amartin@stagleys.demon.co.uk> said:
> Alpha works great if you compile using DEC CC under Digital Unix
> then use the executable.

We've done that before and it works well.  I don't recall serious
crashes on BLAST with that configuration.  There was a bug with
error reporting on exit when using incorrect inputs that I reported
to NCBI last spring.  That's probably fixed by now.

What I wanted to add was:
  1) to do as Andrew suggested you need to statically link the
   executable when compiling under Digital Unix

  2) BLAST can call an external complexity filter and does so with
a call to system().  This requires "sh" to work, and Digitial Unix
hard codes the sh to be in /usr/bin/sh (I think).  Red Hat 5.1 Linux
doesn't have sh in that location (it uses /bin/sh) so we had to make
a symbolic link from one to the other.

						(another) Andrew
						dalke@bioreason.com

From owner-software@net.bio.net Mon Dec 07 22:00:00 1998
Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!dispose.news.demon.net!demon!news.demon.co.uk!demon!cammol1.demon.co.uk!see_sig
From: see_sig@cmtech.co.delete.uk (Richard P. Grant)
Newsgroups: bionet.software
Subject: Re: clustal IS y2k compliant.
Date: Tue, 08 Dec 1998 08:19:21 +0000
Organization: CMT
Message-ID: <see_sig-0812980819370001@192.168.0.84>
References: <74imlf$lsp@news.u-strasbg.fr>
Reply-To: rgrant@netscape.net
NNTP-Posting-Host: cammol1.demon.co.uk
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In article <74imlf$lsp@news.u-strasbg.fr>, jeanmougin@igbmc.u-strasbg.fr wrote:

>         Clustal programs are y2k compliant.
> 
>                 Even if I feel a little bit ridiculous.

Giggle.  Hey, my wristwatch is y2k compliant! :-)

This may interest you, Francois:
http://www.angelfire.com/oh/justanumber/

R

-- 
Richard P. Grant MA DPhil     |             rgrant at cmtech.co.uk
Senior R&D Scientist          |             work: www.cmtech.co.uk
Cambridge Molecular           |      home: www.avnet.co.uk/adastra           
           -- +44 1223 508345 - the Number of the Yeast --

From owner-software@net.bio.net Mon Dec 07 22:00:00 1998
Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.cwix.com!199.0.65.142!news-feed1.tiac.net!posterchild2!news@tiac.net
From: Jennifer Laakso <jlaakso@healthtech.com>
Newsgroups: bionet.software
Subject: Conference on Lead Optimization
Date: Tue, 08 Dec 1998 15:06:18 -0800
Organization: Cambridge Healthtech Institute
Lines: 30
Message-ID: <366DB0EA.2F6C@healthtech.com>
Reply-To: jlaakso@healthtech.com
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We would like to bring to your attention a conference that may be of
interest to your group.

"Smarter LEAD OPTIMIZATION:  Easing the Bottleneck", San Diego,CA, March
18-19, 1999.

Session Topics Include:

Lead Prioritization and Selection
Gene-Based Approaches
Optimization and ADME
Putting It All Together

Early Registration (by January 8, 1999)
Commercial =$795 Academic =$345

Advance Registration (by February 5, 1999)
Commercial =$845 Academic =$395

On-site or Late Registration
Commercial =$945 Academic =$445

For more information please contact:

Cambridge Healthtech Institute
1037 Chestnut St.
Newton Upper Falls, MA 02464

PH: 617-630-1300 - FAX: 617-630-1325 - EMAIL: chi@healthtech.com
WEB: www.healthtech.com

From owner-software@net.bio.net Mon Dec 07 22:00:00 1998
Message-ID: <366D8FD2.4B0A2420@bioreason.com>
Date: Tue, 08 Dec 1998 12:45:06 -0800
From: Andrew Dalke <dalke@bioreason.com>
Organization: Bioreason, Inc.
X-Mailer: Mozilla 4.05 [en] (X11; U; IRIX 6.2 IP22)
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Newsgroups: bionet.software
Subject: Re: clustal IS y2k compliant.
References: <74imlf$lsp@news.u-strasbg.fr> <see_sig-0812980819370001@192.168.0.84> <subbtlf9cph.fsf@unst.sanger.ac.uk>
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Peter Rice <pmr@sanger.ac.uk> mentioned:
> Come to think of it - what does a "millenium countdown clock"
> show when Y2K does arrive? Reset to a Y3K countdown perhaps?

Perhaps there should be a more generic 
"problem with dates"
clock.  There's a list of the hyped date errors somewhere I
saw.  Among others they include:

  Feb 29th does exist in 2000
  Jan. 19th, 2038 contains second (32 bit) MAXINT under C/unix
    (start of "epoch 1")

Or even more generic, "problems with fixed field widths" like
the estimated year:

  we run out of PDB identifiers (2004)
  the US runs out of 10 digit phone numbers (2015??)

Don't think the PDB one is likely to be on a mass market product :)

						Andrew
						dalke@bioreason.com

From owner-software@net.bio.net Mon Dec 07 22:00:00 1998
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From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin)
Newsgroups: bionet.software
Subject: clustal IS y2k compliant.
Date: 8 Dec 1998 08:06:07 GMT
Organization: CRC - Universite Louis Pasteur - Strasbourg France
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	Funny isn't it?

	We are floaded of messages from people who ask : "Is Clustal{X,W} y2k
	compliant ?" . Because we can't answer that this question is quite...
	[Please add your own here], I think I have to officially announce that
	Clustal programs are y2k compliant.

		Even if I feel a little bit ridiculous.

						François.

P.S.: y2k seems to be the geek and most technocratic term for year 2000
P.P.S.: Yes, ClustalX is using a timestamp in the headers of the postscript
file. But this is the system timestamp, nothing is done with it, just copy.
-- 
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France

From owner-software@net.bio.net Mon Dec 07 22:00:00 1998
Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!news.pbi.net!206.190.128.10!newsfeed.yosemite.net!newsfeed.berkeley.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail
From: jean-christophe.ravarini@genebio.com
Newsgroups: bionet.software
Subject: Get a MEDLINE entry ?
Date: Tue, 08 Dec 1998 12:50:32 GMT
Organization: Deja News - The Leader in Internet Discussion
Lines: 16
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Hi,

I need to be able to get a MEDLINE entry,
(from an Access DB, using anything useful)
 via http://www.ncbi.nlm.nih.gov/PubMed/ or using FTP.
Does anyone knows a procedure ?
Any ideas/help appreciated, thanks in advance.

Regards,

--
Jean Christophe Ravarini, Software Developper
mailto:jean-christophe.ravarini@genebio.com

-----------== Posted via Deja News, The Discussion Network ==----------
http://www.dejanews.com/       Search, Read, Discuss, or Start Your Own    

From owner-software@net.bio.net Mon Dec 07 22:00:00 1998
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From: see_sig@cmtech.co.delete.uk (Richard P. Grant)
Newsgroups: bionet.software
Subject: Re: clustal IS y2k compliant.
Date: Tue, 08 Dec 1998 12:20:36 +0000
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In article <subbtlf9cph.fsf@unst.sanger.ac.uk>, Peter Rice
<pmr@sanger.ac.uk> wrote:

> see_sig@cmtech.co.delete.uk (Richard P. Grant) writes:
> > In article <74imlf$lsp@news.u-strasbg.fr>, jeanmougin@igbmc.u-strasbg.fr
> > wrote:
> > >         Clustal programs are y2k compliant.
> > Giggle.  Hey, my wristwatch is y2k compliant! :-)
> 
> Maybe so, but for how long?

Well, OK, so I have to set the date in non-31 day months (leap years as
well as non-leap), but it won't crash when we hit 2000 . . .[0]

> You can buy "millenium countdown clocks" that
> tell you how many days to the start of year 2000 but they only come with a
> "one year guarantee" :-)

That's good, because the millennium proper doesn't start until 2001.

> 
> Come to think of it - what does a "millenium countdown clock" show when
> Y2K does arrive? Reset to a Y3K countdown perhaps?

Now *that* would be a good gimmick.

Richard
[0] it's an analogue watch[1], if you hadn't guessed
[1] with no battery.

-- 
Richard P. Grant MA DPhil     |             rgrant at cmtech.co.uk
Senior R&D Scientist          |             work: www.cmtech.co.uk
Cambridge Molecular           |      home: www.avnet.co.uk/adastra           
                 -- In Ventum Faciens Aquam --

From owner-software@net.bio.net Mon Dec 07 22:00:00 1998
Newsgroups: bionet.software
Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!leeds.ac.uk!news
From: t.j.keen@leeds.ac.uk (T. Jeffrey  Keen)
Subject: Re: Looking for unix program converting medline to bibtex
Message-ID: <t.j.keen-0812981050390001@sjuh-pc146.leeds.ac.uk>
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Date: Tue, 8 Dec 1998 10:46:38 +0000 (GMT)
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Do you mean this:

http://toaster.physik.hu-Berlin.DE/~boeck/Sixpack/index.html

In article <366C0CB6.BF58475B@stud.uni-hannover.de>, Joerg Daehn
<jdaehn@stud.uni-hannover.de> wrote:

> Hi,
> 
> some weeks ago I came across a Webpage for a unix-based, x11-gui program
> which converted medline outputs and others to diverse bibliography
> formats (endnote, bibtex). But unfortunately I didn't bookmark that
> page. Now I can't find it anymore. As I am about to write my thesis and
> wanted to start this week I am a little desperate. Does anybody know
> about a tool like that and it's location on the web? It is supposed to
> be freeware, in beta status and made by a french instiitute/university.
> 
> Thanx
> 
> Joerg

From owner-software@net.bio.net Mon Dec 07 22:00:00 1998
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From: Peter Rice <pmr@sanger.ac.uk>
Newsgroups: bionet.software
Subject: Re: clustal IS y2k compliant.
Date: 08 Dec 1998 09:59:06 +0000
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see_sig@cmtech.co.delete.uk (Richard P. Grant) writes:
> In article <74imlf$lsp@news.u-strasbg.fr>, jeanmougin@igbmc.u-strasbg.fr
> wrote:
> >         Clustal programs are y2k compliant.
> Giggle.  Hey, my wristwatch is y2k compliant! :-)

Maybe so, but for how long? You can buy "millenium countdown clocks" that
tell you how many days to the start of year 2000 but they only come with a
"one year guarantee" :-)

Come to think of it - what does a "millenium countdown clock" show when
Y2K does arrive? Reset to a Y3K countdown perhaps?

-- 
----------------------------------------------------------------------
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-software@net.bio.net Mon Dec 07 22:00:00 1998
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From: Peter Rice <pmr@sanger.ac.uk>
Newsgroups: bionet.software
Subject: Re: clustal IS y2k compliant.
Date: 08 Dec 1998 13:26:24 +0000
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see_sig@cmtech.co.delete.uk (Richard P. Grant) writes:
> In article <subbtlf9cph.fsf@unst.sanger.ac.uk>, Peter Rice
> <pmr@sanger.ac.uk> wrote:
> > You can buy "millenium countdown clocks" that
> > tell you how many days to the start of year 2000 but they only come with a
> > "one year guarantee" :-)
> 
> That's good, because the millennium proper doesn't start until 2001.

Yup - so they are already 366 days out. I'm not celebrating the
millenium until then.  Hope nothing much happens in 2000 otherwise
historians will get terribly confused :-)

Meanwhile - I keep hearing about identifying your pets by implanting
"a chip" in the back of the neck. Wonder whether anyone would believe
a story about these chips not being tested for Y2K compliance ...

-- 
----------------------------------------------------------------------
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-software@net.bio.net Tue Dec 08 22:00:00 1998
Sender: thomas@beagle.bmc.uu.se
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Subject: Re: clustal IS y2k compliant.
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From: Thomas Sicheritz <Thomas.Sicheritz@molbio.uu.se>
Date: 09 Dec 1998 17:04:21 +0100
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hmm alignment = sequences ... hmmmm
 ... where are you going to retrieve your sequences from ?
Beyond six months, you must be (sequence)self-sustaining.
- time to buy a Y2K compliant Sequencer ... :-)

-thomas


From owner-software@net.bio.net Tue Dec 08 22:00:00 1998
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From: Haruna Cofer <haruna@columbus.sgi.com>
Newsgroups: bionet.software
Subject: Parallel CLUSTALW for SGI
Date: Wed, 09 Dec 1998 13:13:20 -0500
Organization: Silicon Graphics, Inc.
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Hello!

I just wanted to let everyone know that Silicon Graphics has
parallelized CLUSTALW 1.74 for SGI systems running IRIX 6.2 and 
higher.  It is freely available for download from this site:

 http://www.sgi.com/chembio/resources/clustalw/

Also available on this site is more information on running 
CLUSTALW on SGI systems, including a General FAQ List, 
Technical FAQ List, Porting Notes, and a Known Problems and 
Fixes page.  You may also be interested in our Bioinformatics 
Benchmark Report, which has performance information on FASTA, 
BLAST (including High Throughput BLAST, which is a modification 
of the original versions of BLAST, designed to run efficiently 
in a high throughput environment), and now CLUSTALW:

 http://www.sgi.com/chembio/resources/bioinformatics/clw1.html

Please note that our parallelized CLUSTALW incorporates a bug 
fix for a memory access bug in the original CLUSTALW distribution, 
so the scores and alignments you get with our parallelized CLUSTALW 
may be different from those you get with the original CLUSTALW.  
This bug has been reported to the authors of CLUSTALW, and more
information about this bug is available on the Known Problems & 
Fixes page for CLUSTALW:

 http://www.sgi.com/chembio/resources/clustalw/problems_and_fixes.html

Thanks, and please do let me know if you have any questions!

-- Haruna  :)

-- 
-------------------------------------------------------------------------- 
  Haruna N. Cofer                           614-855-5245           (tel)
  Corporate Marketing/MSD                   248-848-5653           (fax)
  Silicon Graphics Inc.                     800-859-1020 x4553  (v-mail)
  715 Affirmed Court                        x6-265-4553       (internal)
  Columbus, OH  43230                       haruna@sgi.com      (e-mail)
--------------------------------------------------------------------------

From owner-software@net.bio.net Tue Dec 08 22:00:00 1998
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From: "Steven Jansen" <s.jansen@inter.nl.net>
Newsgroups: 3b.misc,alt.binaries.sounds.wav,alt.cd-rom,alt.comp.software.tools,alt.misc,aol.misc,bionet.software,biz.misc
Subject: Dartpro 32
Date: Wed, 9 Dec 1998 15:18:16 +0100
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    wo has an registered
version for me and who can mail it to me

please help me

steven
s.jansen@inter.nl.net




From owner-software@net.bio.net Tue Dec 08 22:00:00 1998
Path: biosci!email.msn.com!aet_ltd
From: aet_ltd@email.msn.com ("AET Ltd")
Newsgroups: bionet.software
Subject: eco-tox & endocrine detection
Date: 9 Dec 1998 10:34:34 -0800
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This is a multi-part message in MIME format.

------=_NextPart_000_0024_01BE23A1.00C26800
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Has anybody come across any organisations offering screening for =
possible endocrine disruptor compounds using eco-tox tests?

Any info or contacts would be greatly appreciated.

Many thanks
Philip Massey

------=_NextPart_000_0024_01BE23A1.00C26800
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3Dtext/html;charset=3Diso-8859-1 =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.2106.6"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT size=3D2>Has anybody come across any organisations offering =
screening=20
for possible endocrine disruptor compounds using eco-tox =
tests?</FONT></DIV>
<DIV><FONT size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT size=3D2>Any info or contacts would be greatly=20
appreciated.</FONT></DIV>
<DIV><FONT size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT size=3D2>Many thanks</FONT></DIV>
<DIV><FONT size=3D2>Philip Massey</FONT></DIV></BODY></HTML>

------=_NextPart_000_0024_01BE23A1.00C26800--



From owner-software@net.bio.net Tue Dec 08 22:00:00 1998
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From: plxsrt@pln1.nott.ac.uk (Simon R Tomlinson)
Newsgroups: bionet.software
Subject: Re: FASTA format - proposed max line limit
Date: Wed, 09 Dec 1998 13:57:43 GMT
Organization: ACS, The University of Nottingham
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Message-ID: <74lvl5$4g5$1@oyez.ccc.nottingham.ac.uk>
References: <71qtgl$m8u@gap.cco.caltech.edu>    <72e3hu$p86$1@news.fas.harvard.edu> <72hpkf$hoi@gap.cco.caltech.edu>    <72hv4q$h09$1@news.fas.harvard.edu> <72op6t$2fh@news.u-strasbg.fr> <3650DB3D.84898F47@bioreason.com> <72qt83$i6o$1@news.fas.harvard.edu> <36542597.4145C085@bioreason.com> <731l4k$8lp$1@news.fas.harvard.edu> <73eok6$2oo@gap.cco.caltech.edu> <73mjou$tpm$1@news.fas.harvard.edu> <742j7p$jgu$1@news.fas.harvard.edu>
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You really have to consider why Fasta format is so useful and
therefore so commonly used.  One of the reasons for popularity is that
it is a simple file format.    Programs that stuff a lot of details
into the header are bound to make the format more complex.  
I would suggest that if the format becomes more complex then it'll
become less popular.

In an extreme case you could take the header from any sequence record
and stuff it onto a single line.  But surely this is just reinventing
an old format without the end-of-line breaks?!  [and without one
sequence per file].  I don't think this is desirable.

A lot of programs that I use will truncate the long header line anyway
(eg clustalw) so you lose the long header details.   To avoid this I
usually truncate the header myself to give the record a unique
identifier.   I usually use  the accession number or sequence name.
This gives the best of both worlds, the Fasta format remains simple
but I have access to the original record  to retrieve any addiitional
details that I require.  What is wrong with using Fasta this way?

Simon T 


From owner-software@net.bio.net Wed Dec 09 22:00:00 1998
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From: "Dr Andrew Grantham" <A.Grantham@brighton.ac.uk>
Newsgroups: bionet.software
Subject: Endnotes
Date: Thu, 10 Dec 1998 14:43:13 +0000
Organization: CENTRIM, University of Brighton
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I'm new to UoB and am in need of a copy of "Endnote Plus".  I understand
that a message was circulated recently on this subject with a view to a bulk
purchase.  Can anyone help locate the source of this message?

Andrew Grantham
CENTRIM

From owner-software@net.bio.net Wed Dec 09 22:00:00 1998
Message-ID: <366FD841.99D3E905@bioreason.com>
Date: Thu, 10 Dec 1998 06:18:41 -0800
From: Andrew Dalke <dalke@bioreason.com>
Organization: Bioreason, Inc.
X-Mailer: Mozilla 4.05 [en] (X11; U; IRIX 6.2 IP22)
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Newsgroups: bionet.software
Subject: Re: FASTA format - proposed max line limit
References: <71qtgl$m8u@gap.cco.caltech.edu>    <72e3hu$p86$1@news.fas.harvard.edu> <72hpkf$hoi@gap.cco.caltech.edu>    <72hv4q$h09$1@news.fas.harvard.edu> <72op6t$2fh@news.u-strasbg.fr> <3650DB3D.84898F47@bioreason.com> <72qt83$i6o$1@news.fas.harvard.edu> <36542597.4145C085@bioreason.com> <731l4k$8lp$1@news.fas.harvard.edu> <73eok6$2oo@gap.cco.caltech.edu> <73mjou$tpm$1@news.fas.harvard.edu> <742j7p$jgu$1@news.fas.harvard.edu> <74lvl5$4g5$1@oyez.ccc.nottingham.ac.uk>
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Simon R Tomlinson <plxsrt@pln1.nott.ac.uk> said:
> Programs that stuff a lot of details into the header are bound to
> make the format more complex.  I would suggest that if the format
> becomes more complex then it'll become less popular.

I agree, and I don't think anyone else here argues against that
viewpoint.  While there's been no consensus, I've been arguing
that XML should be used as the basis for a more generalized format.
At the very least, it allows Unicode so we can write names properly
with umlauts, tildes, accents, etc.

> In an extreme case you could take the header from any sequence record
> and stuff it onto a single line.  But surely this is just reinventing
> an old format without the end-of-line breaks?!
> [...]
> A lot of programs that I use will truncate the long header line anyway
> (eg clustalw) so you lose the long header details.

The problem comes with intermediate usages of the comment field,
expecially when using software to create those intermediate forms
automatically.  "A lot of programs" will use long header lines.
Consider NCBI's merged FASTA records which combine duplicate records
into one record.  The headers are joined into one line (seperated by
control-A (ASCII 1) characters).  For example, on one line,

| >gi|1469284 (U05042) afuC gene product [Actinobacillus
| pleuropneumoniae]^Agi|1477453 (U04954) afuC gene product
| [Actinobacillus pleuropneumoniae]


> To avoid this I usually truncate the header myself to give the
> record a unique identifier.  I usually use  the accession number
> or sequence name.

  The problem is *you* know which information should be truncated since
you know where the data will be used, but it's quite hard for software
to do that.  Even in this example, should it be truncated to the first
record identifier:

| >gi|1469284

to all record identifiers (note: if there are over about 8 records,
this will also exceed 80 character lines, and there are many cases
(esp. with records from PDB entries) where this can happen):

| >gi|1469284 gi|1477453

or to the 1st 75 characters (arbitrary truncation of text)?
Some people just need a single identifier, some need all of them
(eg, to answer the question "how many duplications of this sequence
exist) and some want to see them all (eg, look at the results of the
NCBI BLAST searches).

Since I cannot think of a good way to truncate comment lines generated
from programs that produce >80 characters, I am convinced that
truncation is not the solution because that will render some
existing programs useless and some data file uninterpretable.  My
proposal of using multiple lines will also render some programs
useless but all existing files can be easily translated to that
format with no loss of content, the file format is only slightly
more complicated than the existing FASTA format, and it is possible
to convert any record to a form where all lines are <80 columns,
if so desired.

						Andrew Dalke
						dalke@bioreason.com

From owner-software@net.bio.net Wed Dec 09 22:00:00 1998
Path: biosci!agate!newsfeed.acns.nwu.edu!news.acns.nwu.edu!news	
From: "Richard J. Schuerger" <charade@nwu.edu>
Newsgroups: bionet.software
Subject: Scopfit
Date: Thu, 10 Dec 1998 12:48:19 -0600
Organization: Northwestern University, Evanston, IL.  USA
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Hi,

I'm trying to find a kinetic modeling program called Scopfit (sp?).

If anyone knows where I could get a copy, please let me know by Email.

Thanks

--
_________________________________________________________________

Richard Schuerger                                 Charade@nwu.edu
Northwestern University                      Voice: (312)503-9810
Dept. of Physiology M211                       FAX: (312)503-5101
303 E. Chicago Ave.,  Chicago, IL 60611
   http://neuroscience.miningco.com
   http://pubweb.acns.nwu.edu/~rjs979/useful.html

Today's Quote (#526)

Common sense is genius dressed in its working clothes.
    - Ralph Waldo Emerson



From owner-software@net.bio.net Thu Dec 10 22:00:00 1998
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From: "John" <us168@usa.net>
Newsgroups: bionet.software
Subject: Software World
Date: 11 Dec 1998 05:02:27 GMT
Organization: The Internet Group Ltd
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Hi, my friends.

Please go to: http://members.tripod.com/~best_web/software.html
You can find a lot of useful software.


From owner-software@net.bio.net Thu Dec 10 22:00:00 1998
Path: biosci!ACCEFYN.ORG.CO!acad
From: acad@ACCEFYN.ORG.CO (Alexander Garcia)
Newsgroups: bionet.software
Subject: inquiry-mailing list
Date: 10 Dec 1998 21:26:18 -0800
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do any of you know where can I download a good mailin list software
(server software) ??? free???


From owner-software@net.bio.net Thu Dec 10 22:00:00 1998
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From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin)
Newsgroups: bionet.software
Subject: Re: Parallel CLUSTALW for SGI
Date: 11 Dec 1998 08:34:14 GMT
Organization: CRC - Universite Louis Pasteur - Strasbourg France
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In article <366EBDC0.446B@columbus.sgi.com>,
	Haruna Cofer <haruna@columbus.sgi.com> writes:

> Please note that our parallelized CLUSTALW incorporates a bug 
> fix for a memory access bug in the original CLUSTALW distribution, 
> so the scores and alignments you get with our parallelized CLUSTALW 
> may be different from those you get with the original CLUSTALW.  
> This bug has been reported to the authors of CLUSTALW, and more
> information about this bug is available on the Known Problems & 
> Fixes page for CLUSTALW:
> 
>  http://www.sgi.com/chembio/resources/clustalw/problems_and_fixes.html

	In fact, this bug does just affect the scores of some alignments and
should not the accuracy of the alignment. In fact, this is fixed in the 1.65b
version of ClustalX. Will be incorporated as soon as possible in
ClustalW.

	Thanks for this bug fix and for the SGI parallel version.

							François.
-- 
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France

From owner-software@net.bio.net Thu Dec 10 22:00:00 1998
Message-ID: <3671AB7D.431ED347@bioreason.com>
Date: Fri, 11 Dec 1998 15:32:13 -0800
From: Andrew Dalke <dalke@bioreason.com>
Organization: Bioreason, Inc.
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Newsgroups: bionet.software
Subject: Re: Formating DB's for BLAST on NT
References: <36717745.82451298@news.ucsf.edu>
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Richard <rjacob-nospam@itsa.ucsf.edu> asked:
> For BLAST to use the database it needs to be formated with
> the "formatdb" program. Unfortunately I always obtain an error:
> [...]
> Does anyone have any clues to what I might be doing wrong or
> not doing?

If I recall, you need to have a .ncbirc (or equivalent) for
that to work.  Browsing NCBI for a bit, I think there are relevent
comments in:

  ftp://ncbi.nlm.nih.gov/blast/executables/README

Look for
> This is specified by the main configuration file for the NCBI
> toolkit (".ncbirc" on UNIX systems, ncbi.ini on Windows, analogous
> names on other platforms).

  I know, it's documentation for BLAST but I recall needing that
file for formatdb to work; probably because they are all built
from the same toolkit.

						Andrew
						dalke@bioreason.com

From owner-software@net.bio.net Thu Dec 10 22:00:00 1998
Path: biosci!biosci!not-for-mail
From: oguz@rift.foo.net (Oguz Yetkin)
Newsgroups: bionet.general,bionet.neuroscience,bionet.software,bionet.software.resources,sci.bio.technology,sci.misc,comp.ai.neural-nets
Subject: Neuroanatomy of C. elegans for Computation (need software)
Date: 11 Dec 1998 14:58:43 -0800
Organization: California Institute of Technology, Pasadena
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Xref: biosci bionet.general:31843 bionet.neuroscience:26437 bionet.software:22488

Hello,

I hope this is not off-topic for any of your groups.

I recently got a hold of _AY's Neuroanatomy of C. elegans for Computation_
by Achacoso and Yamamoto (1992).  I am interested in experimenting with an
artificial neural network model based on the neuroanatomy of C.elegans, and
the book does come with two disks.

Unfortunately, the disks are old 5.25 low density disks, and have been rendered
unreadable by time.

Does anyone have information on where I can find the data/software contained
on these disks on the internet or somehow contact the authors (a night
of web searching has been rather fruitless).  If not, any information pointing to neural net data based on actual anatomy would be appreciated.

Please e-mail all responses

thanks in advance


Oguz Yetkin
oguz@rift.foo.net
 


From owner-software@net.bio.net Thu Dec 10 22:00:00 1998
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From: rjacob-nospam@itsa.ucsf.edu
Newsgroups: bionet.software
Subject: Formating DB's for BLAST on NT
Date: Fri, 11 Dec 1998 20:06:33 GMT
Organization: UCSF, ITS
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I'm trying to set up an in lab BLAST server on an NT box using NCBI
BLAST version 2.0. I've unpacked the programs and downloaded a few
databases. For BLAST to use the database it needs to be formated with
the "formatdb" program. Unfortunately I always obtain an error:

================[ Dec 11, 1998 11:45 AM ]========================
Version 2.0.6 [Sept-16-1998]
Started database file "D:\Blast\ecoli_aa"
FATAL ERROR: [067:001] FindPath failed
FATAL ERROR: [067:000] Failure to read sequence. FastaToSeqEntry()
failed.

Formated 0 sequences


Does anyone have any clues to what I might be doing wrong or not
doing?
The databases used are amino acid databases in FASTA format from the
NCBI. I've tried variations of all the options in "formatdb" to no
improvement. The documentation I have read did not mention this
problem or any other special procedures that i must do before using
the database.

Thanks in advance for you help.

Richard  




From owner-software@net.bio.net Thu Dec 10 22:00:00 1998
Message-ID: <36716308.D6DBA79D@wolfram.com>
Date: Fri, 11 Dec 1998 12:23:04 -0600
From: Wolfram Research <news@wolfram.com>
Organization: Wolfram Research, Inc. 
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Subject: Mathematica Link for Excel
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Mathematica Link Adds Math Power to Excel

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Mathematica Link for Excel is available for Windows and Macintosh
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From owner-software@net.bio.net Thu Dec 10 22:00:00 1998
Path: biosci!news.stanford.edu!logbridge.uoregon.edu!sunqbc.risq.qc.ca!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail
From: richard_steinman@cmagroup.com
Newsgroups: bionet.software
Subject: Florida; Staff Scientist/Engineer; Electrophysiology, Algorithms, Signal Processing
Date: 11 Dec 1998 16:35:35 GMT
Organization: Career Marketing Associates
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Florida; Staff Scientist/Engineer; Electrophysiology, Algorithms, Signal 
Processing
-Senior Software Engineer
-Florida
-Salaried, Full-Time, Excellent Benefits
(Excellent Relocation Package Available)

This professional will be actively involved in leading advanced cardiovascular 
EP product development.  Ideal candidate will have PhD/MS in either Biomedical 
Engineering, CS, EE, Physics or Computer Science with a solid clinical 
appreciation of cardiovascular electrophysiology.  Technical skills should 
include: Advanced algorithms, signal processing and software development. 
Experience with Windows NT, Win32  and  C/C++ skills would be a plus. 
Must bring in EP expertise either through engineering, or through the 
science route; preferably both. Ideal candidate will  have industrial, 
or have collaborated in an industrial product development effort.  Technical 
leadership/mentoring experience would also be helpful.


Please refer to JO# 7216RJS in your response.

richard_steinman@cmagroup.com 

Richard Steinman; Team Leader
Career Marketing Associates
rjs@cmagroup.com
Staffing & Consulting Solutions Since 1968

From owner-software@net.bio.net Thu Dec 10 22:00:00 1998
Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!europa.clark.net!206.132.26.41!newsfeed-east.supernews.com!supernews.com!Supernews69!not-for-mail
From: "Pearce" <smithwip@ccmail.orst.edu>
Newsgroups: bionet.software
Subject: Drawing Plasmid Maps
Date: Fri, 11 Dec 1998 02:46:10 -0800
Organization: Posted via RemarQ, http://www.remarQ.com - Discussions start here!
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Could anyone recommend a decent freeware/shareware program for drawing
plasmid maps?

Thanks!



From owner-software@net.bio.net Thu Dec 10 22:00:00 1998
Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!wn3feed!worldnet.att.net!135.173.83.225!attworldnet!newsadm
From: "Robert Corriveau" <Robert.Corriveau@worldnet.att.net>
Newsgroups: bionet.software
Subject: RE:CATALOG
Date: 11 Dec 1998 21:02:51 GMT
Organization: AT&T WorldNet Services
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Anybody interested in an inexspensive software source.Send me an
e-mail,just write in it send free catalog. File has thousands of
listings,all prices under $10.00.


From owner-software@net.bio.net Fri Dec 11 22:00:00 1998
Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!netnews.com!news2.euro.net!news.telekabel.nl!not-for-mail
From: "rob willemse" <rowi@telekabel.nl>
Newsgroups: bionet.software
Subject: FTP superfast
Date: Sat, 12 Dec 1998 16:36:53 +0100
Organization: TeleKabel
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Go here for free and shareware very fast cable modem 300kbs
http://friesland.telekabel.nl/~rowi
push FTPserverbutton.



From owner-software@net.bio.net Fri Dec 11 22:00:00 1998
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From: "tendo" <tendo@fas.harvard.edu>
Newsgroups: bionet.software
Subject: Fasta Sequence class
Date: Sat, 12 Dec 1998 01:13:38 -0500
Organization: Harvard University, Cambridge, Massachusetts
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Referen