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From owner-bio-software@hgmp.mrc.ac.uk  Sat Apr  1 11:18:02 2000
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From: aries@clara.co.uk ("Ian Campbell")
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This is a multi-part message in MIME format.

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Hi

Is Photo Slider available to download from the Web?

Thanks

Ian

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content=3D"text/html; charset=3Diso-8859-1" =
http-equiv=3DContent-Type>
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<DIV><FONT face=3D"Arial Narrow" size=3D3>Hi</FONT></DIV>
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Web?</FONT></DIV>
<DIV>&nbsp;</DIV>
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<DIV>&nbsp;</DIV>
<DIV><FONT face=3D"Arial Narrow">Ian</FONT></DIV></BODY></HTML>

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From owner-bio-software@hgmp.mrc.ac.uk  Sat Apr  1 11:30:20 2000
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From: anbarasu@my-deja.com
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Hi,

   I am having an alignment file that is a output from
   SAGA. I would like to convert it into MSF format.
   Could some one help me?

Thanks in advance.
Truly
anbarasu l.a.


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


From owner-bio-software@hgmp.mrc.ac.uk  Mon Apr  3 11:01:06 2000
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Send an email with "THE LIST" in the subject line to

auto.program.list@iname.com  Or  bigbrian@writemail.com

"SoftWare For P.C, Apple Macintosh,  Playstation & MP3 Music"

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





From owner-bio-software@hgmp.mrc.ac.uk  Mon Apr  3 13:17:07 2000
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Hi peeps,

Please excuse the x-post.  Which secondary structure prediction method 
is generally reckoned the 'best' these days.  I know about 
http://www.EMBL-Heidelberg.DE/predictprotein/  would appreciate any 
other pointers.

Cheers,

Richard

-- 
Richard P. Grant MAD Phil          http://www.gerbil.org.uk/
Please reply to rpg 'at' mrc-lmb.cam.ac.uk

'There's a fine line between genius and just farting around'


From owner-bio-software@hgmp.mrc.ac.uk  Mon Apr  3 13:27:46 2000
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Subject: Re: Parsing out ORFs?
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In article <38E3826A.6A8CE0AA@nospam.net>,  <nospam@nospam.net> wrote:
>Is there an "out of the box" method for producing separate sequence
>lines for each ORF in a genomic sequence?  Something suitable for making
>a multisequence fasta file would be nice.

Try 'getorf' in the EMBOSS package.

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




From owner-bio-software@hgmp.mrc.ac.uk  Mon Apr  3 14:45:56 2000
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From: Mark Berres <markb@ravel.zoology.wisc.edu>
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Dear Readers,

I have made available a software application, exTRACE, designed specifically
to extrace data records from ABI derived tracefiles (chromatograms) and
write them to separate files in a user selectable format (hex, bin or dec).
Pre-compiled binaries are availble for Unix (Solaris 2.7), DOS and 
Macintosh platforms. Also included with each package are two PDF files
describing 1. the organization of ABI tracefiles (directed primarily toward
programmers) and 2. descriptions of available data records (FLAGS) in ABI
GeneScan tracefiles. Although I focus on GeneScan type data, exTRACE works on
any tracefile processed with ABI software (e.g. 373, 377, 310 and 3700).

If interested, see the Bioinformatics sub-section at my website
http://ravel.zoology.wisc.edu/sgaap 

				Thanks,

					Mark

-- 
Mark E. Berres
University of Wisconsin-Madison



From owner-bio-software@hgmp.mrc.ac.uk  Mon Apr  3 15:26:02 2000
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From: letondal@nefertiti.pasteur.fr (Catherine  Letondal)
X-Newsgroups: bionet.molbio.proteins,bionet.software
Subject: Re: 2ndry structure prediction
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In article <rgrant-1CDB0A.13164903042000@nntp-serv.cam.ac.uk>, "Richard P. Grant" <rgrant@netscape.net> writes:
>Hi peeps,
>
>Please excuse the x-post.  Which secondary structure prediction method 
>is generally reckoned the 'best' these days.  I know about 
>http://www.EMBL-Heidelberg.DE/predictprotein/  would appreciate any 
>other pointers.

Try:
http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?english=1&query=second&bio=structural+biology

(BioNetbook: http://www.pasteur.fr/recherche/BNB/bnb-en.html)

-- 
Catherine Letondal -- Pasteur Institute Computing Center


From owner-bio-software@hgmp.mrc.ac.uk  Tue Apr  4 07:45:14 2000
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From: Przemko Tylzanowski <przemko@med.kuleuven.ac.be>
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Subject: Re: ABI data extraction utilities
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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
&nbsp;
<p>Mark Berres wrote:
<blockquote TYPE=CITE>Dear Readers,
<p>I have made available a software application, exTRACE, designed specifically
<br>to extrace data records from ABI derived tracefiles (chromatograms)
and
<br>write them to separate files in a user selectable format (hex, bin
or dec).
<br>Pre-compiled binaries are availble for Unix (Solaris 2.7), DOS and
<br>Macintosh platforms. Also included with each package are two PDF files</blockquote>
SNIP...
<p>Is there a Windows version? What is DOS besides Denial Of Service ?
<br>Przemko
<p>--
<br>Przemko Tylzanowski Ph.D.
<br>LSD &amp; Joint
<br>O &amp; N
<br>University of Leuven
<br>Herestraat 49
<br>3000 Leuven
<br>Belgium
<p>phone: (32-16)34-61-96
<br>fax&nbsp; : (32-16)34-62-00
<br>&nbsp;</html>



From owner-bio-software@hgmp.mrc.ac.uk  Tue Apr  4 08:55:27 2000
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Hi again,

http://globin.bio.warwick.ac.uk/psipred/

looks pretty good, gave good results on a known structure too.

Thanks everyone.

R

-- 
Richard P. Grant MAD Phil          http://www.gerbil.org.uk/
Please reply to rpg 'at' mrc-lmb.cam.ac.uk

'There's a fine line between genius and just farting around'


From owner-bio-software@hgmp.mrc.ac.uk  Tue Apr  4 12:47:59 2000
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From owner-bio-software@hgmp.mrc.ac.uk  Tue Apr  4 17:20:15 2000
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From: tmark@my-deja.com
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Subject: Bio::DB::GenBank and http proxy ?
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I had a script which used Perl and LWP to get sequences by accession
number.  This script has mysteriously started to fail (I get errors like
qmap - need URL-param for request processing), so I tried to get
Bio::DB::GenBank working, hoping to see whether its get_Seq_by_acc
routine would work.

But, the BioPerl modules (or these routines at least) do not seem to
support proxying.  Has anybody been able to get this stuff to work with
through an http proxy ?  Are the changes non-trivial ?

thanks for any pointers,
terry


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


From owner-bio-software@hgmp.mrc.ac.uk  Tue Apr  4 19:58:04 2000
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From: "rop35602" <rui.c.melo@mail.telepac.pt>
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I am looking for a program that allows me to measure areas  and distances in
a digitised image.



Thank you for reading my message

Rui Melo
rui.c.melo@mail.telapc.pt



begin 666 RUI COSTA MELO.vcf
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'5D-!4D0-"@``
`
end



From owner-bio-software@hgmp.mrc.ac.uk  Wed Apr  5 03:00:16 2000
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From: markb@ravel.zoology.wisc.edu (Mark Berres)
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In article <38E98FA0.7658DDBF@med.kuleuven.ac.be>,
	Przemko Tylzanowski <przemko@med.kuleuven.ac.be> writes:
> <p>Is there a Windows version? What is DOS besides Denial Of Service ?

Dr. Tylzanowski,

	I do not have available any windows application at
this time. However, assuming that you have Windows 98 or
later, you should have a DOS shell installed. No denial of service
here; DOS is (or was, depending) an acronym for "Disk Operating 
System" of pre-graphical operating systems. To run extrace, enter
the "programs" menu under the start option and choose the MS-DOS
prompt option. Change to the directory where you uncompressed
the files and type extrace to invoke the program.

			Sincerely,

					Mark

-- 
Mark E. Berres
University of Wisconsin-Madison
http://ravel.zoology.wisc.edu/sgaap


From owner-bio-software@hgmp.mrc.ac.uk  Wed Apr  5 10:52:59 2000
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From: Nicolas Le Novere <nl223@cus.cam.ac.uk>
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"Richard P. Grant" wrote:

> Please excuse the x-post.  Which secondary structure prediction method
> is generally reckoned the 'best' these days.  I know about
> http://www.EMBL-Heidelberg.DE/predictprotein/  would appreciate any
> other pointers.

see http://www.pasteur.fr/recherche/unites/neubiomol/ secstrpr.html
for pointers, references and a little discussion.

Important: use SEVERAL programs, based on DIFFERENT approaches 
See the result of JPRED with PHD+DSC+NNSSP+PREDATOR

Currently the best are:

->statistical information (GOR, hydrophobicity etc ...)
	DSC - It is not maintained anymore, because its son, PROF
is launched. However nothing is published. You can find DSC on the
pasteur website. Q3 ~ 70-72

->nearest-neighbor (~similarity with protein of know structures)
	NNSSP    Q3 ~ 68-72

->neural-networks
	JNET
	PSIPRED - it is a sort of reimplementation of PHD, with a 
currated alignment as input, and a better training. Q3 up to 76%

->hmm
	SAM99, aimed to be a fold-recognition program, can provide
good secondary structure predictions.

--
Dr Nicolas Le Novère                   e-mail: nl223@cus.cam.ac.uk 
Dpt Zoology, Univ Cambridge, Downing street, Cambridge CB2 3EJ, UK

tel: +44 1223 336623                          fax: +44 1223 336676


From owner-bio-software@hgmp.mrc.ac.uk  Wed Apr  5 10:55:32 2000
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From: Nicolas Le Novere <nl223@cus.cam.ac.uk>
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Hello,

I am new to bioperl. I successfully wrote scripts with Seq.pm or
SeqIO.pm, but I can't get the both working together. If anybody
has scripts to send me, I would be delighted to use it as a 
starting point.

Thanks,

--
Dr Nicolas Le Novère                   e-mail: nl223@cus.cam.ac.uk 
Dpt Zoology, Univ Cambridge, Downing street, Cambridge CB2 3EJ, UK
http://www.pasteur.fr/recherche/unites/neubiomol/ 
tel: +44 1223 336623                          fax: +44 1223 336676


From owner-bio-software@hgmp.mrc.ac.uk  Wed Apr  5 12:30:10 2000
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From: andy.vierstraete@rug.ac.be (Andy Vierstraete)
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Problem :

When you are working with different programs for phylogenetic research, you may
have the problem that some programs use the complete species names
(Treeconw), other will use the first 30 characters (Clustalw), and some will
only use the first 10 characters (programs that work with Phylip files like
Puzzle, fastDNAml, ...). For the final result, everybody wants a tree with
complete names, but for most analyses, you have to shorten the names to 10
characters, and afterwards, you have to complete the names again. A lot of time
is wasted that way, not mentioning the boring job to do this... Cutoff does this
work for you... :-)

http://allserv.rug.ac.be/~avierstr/programs/programs.html

Written by Andy Vierstraete
University of Gent
Department of Biology
K.L. Ledeganckstraat 35
9000 Gent
Belgium
Email : Andy.Vierstraete@rug.ac.be


From owner-bio-software@hgmp.mrc.ac.uk  Wed Apr  5 13:44:50 2000
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From: "Richard J. Dudley" <rdudley@pitt.edu>
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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
Have you tried Chromas?
<br><A HREF="http://www.technelysium.com.au/chromas.html">http://www.technelysium.com.au/chromas.html</A>
<p>or BioEdit?
<br>&nbsp;
<p><A HREF="http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html">http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html</A>
<blockquote TYPE=CITE>Is there a Windows version? What is DOS besides Denial
Of Service ?
<br>Przemko</blockquote>
</html>



From owner-bio-software@hgmp.mrc.ac.uk  Wed Apr  5 15:00:35 2000
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Subject: Re: ABI data extraction utilities
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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
I use Chromas (the freeware version) and am very happy with it. The thing
is that sometimes I would like to see the raw data because the ABI sometimes
miscalls the bases. Now, our lab is PC based and the only Mac is with ABI.
So it would be much more convenient to look at the raw data on PC. I have
somewhere a hack for it but I thought perhaps someone managed a program
to read not only&nbsp; the processed data but also the real trace.
<p>"Richard J. Dudley" wrote:
<blockquote TYPE=CITE>Have you tried Chromas?
<br><a href="http://www.technelysium.com.au/chromas.html">http://www.technelysium.com.au/chromas.html</a>
<br>or BioEdit?
<br><a href="http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html">http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html</a></blockquote>
Przemko</html>



From owner-bio-software@hgmp.mrc.ac.uk  Wed Apr  5 17:01:02 2000
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This message has been posted by:  m.mitchell@REMOVE-THIS-TO-SENDicrf.icnet.uk (Mike Mitchell)

I am interested in finding some software for DOS or Win95/98 that checks
PCR primers against the traget sequence, and each other, much like Bill
Engels' application Amplify for the Mac.

Thanx in advance for your time and help.

If you wish to email a response you'll need to use m.mitchell@icrf.icnet.uk
as our news server has recently start to use spam protection measures.

TTFN

-- 
Michael Mitchell                 "Smoke me a kipper,
User Support                  I'll be back for breakfast."
Molecular Biology Software      Ace Rimmer, Test Pilot
+44 (0)171 269 3115                BBC-TV Red Dwarf           ENFJ


From owner-bio-software@hgmp.mrc.ac.uk  Wed Apr  5 17:20:23 2000
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Dear Colleague,

We are  pleased to announce that, at  last, a new  release (2000.0) of
our  package is  now  available for  Unix.  From  this release onwards
ftp will be the primary method for obtaining the Staden package. Those
for whom this proves difficult can request  a copy on CDROM which will
be sent free of charge.

In either case  the software will only work  in demonstration mode and
will require a licence key to  make it fully functional. These licence
keys are free to academics. They can be requested from:
http://www.mrc-lmb.cam.ac.uk/pubseq/licence.html

The package is available from:

ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/downloads/staden_OS_RELNUM.tar.gz

where OS is one  of alpha (Tru64), linux, sgi  (IRIX) or  solaris; and
RELNUM is the release number (e.g. 2000.0).

For example:
ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/downloads/staden_solaris_2000.0.tar.gz

The files can also be located via
http://www.mrc-lmb.cam.ac.uk/pubseq/downloads.html

For  further information and  a link to  the list  of  changes in this
release please read:

http://www.mrc-lmb.cam.ac.uk/pubseq/whats_new.html

Staden Admin

--

Staden Package Administration         mailto:staden-admin@mrc-lmb.cam.ac.uk
MRC Laboratory of Molecular Biology,  http://www.mrc-lmb.cam.ac.uk/pubseq/
Hills Road,
Cambridge,  CB2 2QH, UK.





From owner-bio-software@hgmp.mrc.ac.uk  Wed Apr  5 20:31:55 2000
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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
What do you mean the "raw data"?&nbsp; I don't have an automated sequencer,
so the only data I know of is the electropherogram I get from my sequencing
facility.&nbsp; I know that ABI miscalls the bases, but I can print out
the electropherogram and check it that way.&nbsp; Are there other data
that are compiled into the electropherogram?
<p>rich
<p>Przemko Tylzanowski wrote:
<blockquote TYPE=CITE>I use Chromas (the freeware version) and am very
happy with it. The thing is that sometimes I would like to see the raw
data because the ABI sometimes miscalls the bases. Now, our lab is PC based
and the only Mac is with ABI. So it would be much more convenient to look
at the raw data on PC. I have somewhere a hack for it but I thought perhaps
someone managed a program to read not only&nbsp; the processed data but
also the real trace.</blockquote>
</html>



From owner-bio-software@hgmp.mrc.ac.uk  Wed Apr  5 22:57:40 2000
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"Przemko Tylzanowski" <przemko@med.kuleuven.ac.be
> wrote in message news:38EB475D.B546C7D3@med.kuleuven.ac.be...
>I use Chromas (the freeware version) and am very happy with it.
> The thing is that sometimes I would like to see the raw data 
>because the ABI sometimes miscalls the bases. Now, our lab 
>is PC based and the only Mac is with ABI. So it would be 
>much more convenient to look at the raw data on PC. I have
>somewhere a hack for it but I thought perhaps someone 
>managed a program to read not only
>the processed data but also the real trace.
>"Richard J. Dudley" wrote:
>Have you tried Chromas?

>http://www.technelysium.com.au/chromas.html
>or BioEdit?

>http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html

Hi,
there is a pc version for chromas which works very nice. 
It lets you view , edit , save the ABI called bases. If you choose
"export" in the "file" menue it will save the raw fluorescent data.

Bioedit can do the same ; it will,however, not save the raw flu. data.

I also tried exTRACE of Mark Berres. I found it very usefull as
it extracts all the data , not only the raw fluorescense.
(yes Richard , there is a lot more in the ABI file) It works
perfectly in a dos window as he describes in this thread.

-- 
Gys






From owner-bio-software@hgmp.mrc.ac.uk  Thu Apr  6 00:10:23 2000
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From: Nirav Merchant <nirav@arl.arizona.edu_no_spam>
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Try phred for base calling ..its also will spit out quality values

..if you really want the "raw" signal values you can check my site
..this on line utility will output the bases and signal values as a
comma seperated files from a ABI trace file. [ I wrote this so that our
group could create nice traces in vector format for publication
..instead of bitmap screen dumps ].

http://bcf.arl.arizona.edu/tools/abi-upload.php3

I will be happy to give you the source code.


regards,
Nirav


Przemko Tylzanowski wrote:

> I use Chromas (the freeware version) and am very happy with it. The
> thing is that sometimes I would like to see the raw data because the
> ABI sometimes miscalls the bases. Now, our lab is PC based and the
> only Mac is with ABI. So it would be much more convenient to look at
> the raw data on PC. I have somewhere a hack for it but I thought
> perhaps someone managed a program to read not only  the processed data
> but also the real trace.
>
> "Richard J. Dudley" wrote:
>
>> Have you tried Chromas?
>> http://www.technelysium.com.au/chromas.html
>> or BioEdit?
>> http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html
>
> Przemko



From owner-bio-software@hgmp.mrc.ac.uk  Thu Apr  6 22:30:38 2000
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From: Kurt Sims <sspamims@uspamcalgary.ca>
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Subject: Simple graph reading software
Date: Thu, 06 Apr 2000 15:28:05 -0600
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Hi

I'm looking for a nice simple program that will let me plot the points 
for a scattergram, give it a best fit line and then read an unknown.  I 
would love to hear some suggestions.

All I need it to do is accept the standards for the X axis and Y axis 
and then give me the reading when I give it an unknown reading off of 
one of the axis.

The program can be either PC or Mac based, or even on the web.

TIA for any suggestions.

Kurt

-- 
To reply by email please remove the two spams out of my return address.


From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 05:19:52 2000
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Greetings:

I'm looking for a Windows NT program that has some of the capabilities
that I have only been able to find so far in ABI's Sequence Navigator
program that only runs on Macs.  Specifically, I would like to be able
to display an alignment between two DNA sequences.  In addition, I want
to create and display the amino acid translations of both sequences in
the same alignment (formatted above their respective DNA sequences) so
that I can immediately see nucleotide substitutions and the resulting
amino acid substitutions, if present.

Any ideas?

Ron Kagan
kaganr@compuserve.com


From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 06:35:09 2000
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Kurt Sims wrote:
> 
> I'm looking for a nice simple program that will let me plot the points
> for a scattergram, give it a best fit line and then read an unknown.  I
> would love to hear some suggestions.
> 
> All I need it to do is accept the standards for the X axis and Y axis
> and then give me the reading when I give it an unknown reading off of
> one of the axis.
> 
> The program can be either PC or Mac based, or even on the web.

Any decent statistical program should be able to do that. In R (or
S-plus) you can do like this:

> conc <- c(0.5,1,1.5,2)
> reading <- c(15.2,30.2,44.6,59)
> standard <- lm(conc~reading)
> summary(standard)

Call:
lm(formula = conc ~ reading)

Residuals:
        1         2         3         4 
 0.006096 -0.008255 -0.002032  0.004191 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)    
(Intercept) -0.0273051  0.0099380  -2.748    0.111    
reading      0.0342901  0.0002444 140.296 5.08e-05 ***
---
Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 

Residual standard error: 0.007969 on 2 degrees of freedom
Multiple R-Squared: 0.9999,     Adjusted R-squared: 0.9998 
F-statistic: 1.968e+04 on 1 and 2 degrees of freedom,   p-value:
5.08e-05 

> predict(standard,data.frame(reading=38.3))
[1] 1.286005

That is, for reading=38.3 the `standard' predicts a concentration of
1.29.

With the following command, you get more information than you want
(i.e., the confidence intervals of your prediction: usually they are
wider than you want to believe):

> predict(standard,data.frame(reading=38.3),interval="prediction")
          fit      lwr      upr
[1,] 1.286005 1.247655 1.324354

Yes, of course you can omit the intercept and and get the standard line
go through the origin. And of course, you can get all your readings in
one run, just put them in a vector in a data.frame.

cheers, j.oksanen
--
J.Oksanen -- UHLA (University of Helsinki at Lahti)
C-h i m emacs RET m text RET m formatted RET
"GNU Emacs is evil." Linus Torvalds


From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 07:00:15 2000
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Hi,

I have several kb of the 5' untranslated region of a gene.  Is there any
software out there that can do some preliminary analysis of this
sequence for me?  Is there any such resources in the Web.

Specifically I'd like to look for response elements, transcription factor
binding sites, TATA, CAAT boxes and the like.  It seems like a pretty
basic problem and a fairly mechanical process so I would be surprised if
there were not publicly available resources.

Presently I am looking for such things by hand but have found this method
to be unreliable, both because the bias of the observer (myself) possibly
tipping the results in one direction and my inability to search for all
such elements tipping results in the other.


I'd really appreciate the help as I am on a deadline to present my very
preliminary results.  Reply here and/or my regular email address at
ilir@gis.net.


Thanks a lot.


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


From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 08:09:07 2000
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> 
> I am looking for a program that allows me to measure areas  and distances in
> a digitised image.
> 

take a look at NIH-image: 

http://rsb.info.nih.gov/nih-image/

which is a Mac program, or its Window 95 'clone', Scion image

http://www.scioncorp.com/

Both can be freely downloaded

Jan Ruijter


From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 08:15:26 2000
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Hello,
does anybody know a free softeware, which find
restrictions sites in a DNA sequence?

Thanks

Andreas




From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 09:34:38 2000
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From: emsch@its.caltech.edu (Erich Schwarz)
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Hello all,

    I am trying to compile MoST (Tatusov et al., PNAS 91, 12091-12095) 
from source code on Red Hat Linux 6.1.  That requires compilation of 
several other packages first, which date from ~1994.  I have found part 
of what I think I need in:

        ftp://ftp.ncbi.nlm.nih.gov/pub/blast/old/

but this archive lacks an ncbi.tar.Z file of equivalent date
(version 1.4.9 of the BLAST programs, posted on May 6, 1995).  Does
anybody out there have an copy of such a file archived elsewhere, and 
if so, how could I get it?  I did find the archive:

        http://blast.wustl.edu:81/blast-1.3/ncbi/

    But its ncbi toolbox is pretty thin: by its own description, "The 
skeletal library presently contains only C language header (.h) files 
to adapt the BLAST software to various computing platforms..."  I have 
already tried this with MoST, and it hangs.

    If anybody has archived source code containing the complete ncbi 
toolbox from the time of BLAST 1.4, I'd be delighted to try it.  Better 
yet would be somebody who'd already gotten MoST to compile on Linux, of 
course, but given my own experiences I'm not holding my breath...


--Erich Schwarz / emsch@its.caltech.edu


From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 10:36:34 2000
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From: friard@molinette.unito.it (Olivier Friard)
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Hi,

If you are using Windows9x/NT/2000, you can try AnnHyb at
http://annhyb.free.fr
PLEASE NOTE that AnnHyb is not a FREEWARE but is a SHAREWARE. You can
use it for 30 days and after you must register (cost 30 USD)

Bye

Olivier Friard

>does anybody know a free softeware, which find
>restrictions sites in a DNA sequence?



From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 11:48:28 2000
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Dear Readers,

I recently posted versions of exTRACE for Linux and HP-UX. I
expect that by Monday, I will have an SGI version as well.
See the Bioinformatics section at http://ravel.zoology.wisc.edu/sgaap
for further information.

There seems to be a little confusion about what exTRACE is
all about- it is simply a utility that allows the extraction
of data records contained within ABI processed tracefiles
(not gelfiles; I have not finished testing exGEL). Please
refer to the document "377GSFLAGS.pdf" (included with the
exTRACE distribution) for an explanation of typically available 
FLAG records. Although this document described FLAGS present
in GeneScan tracefiles, it is applicable to sequencing-based
tracefiles derived from the ABI 310, 377, and 3700 to the
extent of FLAG overlap (see the posted FLAG dumps).

As an example, FLAG DATA, TAGS 1, 2, 3, and 4 correspond
to the RAW photometric data for filters 0, 1, 2, and 3 when ABI's 
GeneScan or Sequencing software extracted a tracked lane.
DATA TAGS 5, 6, 7, and 8 are records for gel runtime voltage,
current, power and temperature. DATA TAGS 9, 10, 11, and 12
are where the PROCESSED photometric data for filters 0, 1, 2,
and 3 are stored. In a broad sense, processed means (a) multi-
componented, (b) baselined, and (c) whatever else ABI does
to the RAW data. Typically, most software that displays ABI
tracefile data (e.g. Chromas, EditView etc.) shows you only the
processed data.

Thank you for your interest in this program. Comments regarding
its performance and any of the accompanying documentation are
appreciated.

				Sincerely,

					Mark 

	
-- 
Mark E. Berres
University of Wisconsin-Madison
http://ravel.zoology.wisc.edu/sgaap



From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 13:13:39 2000
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Hello,

>does anybody know a free softeware, which find
>restrictions sites in a DNA sequence?

there is a simple program on the net:
http://www.enzim.hu/~tusi/restric/restenzyme.html

You can make simple searching, and can search restrictions sites with
silent mutations too (if the sequence is an ORF).

Gabor E. Tusnady, PhD                   | e-mail:            tusi@enzim.hu
Institute of Enzymology, BRC            | www:   http://www.enzim.hu/~tusi
Hungarian Academy of Sciences           | tel:         (36-1) 466-6533/158
H-1113 Budapest Karolina ut 29, HUNGARY | fax:             (36-1) 466-5465




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Dear Gurus:

I am a Ph.D. student in Molecular Biology and have a plan to persue a career
in Bioinformatics. I have a strong background in Javascript/html and I am
quite comfortable with C and Perl. I want to learn a "real programming
language" and not being able to choose between Java and C++. On one hand
Java has the advantage of being platform-independent and writing a GUI based
program in Java is very easy. On the flip side Java is extremely slow and
migration into system level programming is almost impossible. On the other
hand, C++ will be an eternal language and particularly with increasing
popularity of Linux will be an important language in the days to come and
writing elementary GUI with platform independent toolkits like wxWindows are
not very difficult.

Under such circumstances I'd appreciate your comments in this regard. Which
language will be "the language" in Bioinformatics, Java or C++?

Thank to you all who will help in shaping up my career!

Malay

Malay Kumar Basu
Centre for Cellular and Molecular Biology
Hyderabad 500007
I N D I A

Fax: (00-91)40-7171195
Phone: (00-91)40-7172241
-----
Cataholic: Can't stop bringing cats home.
-----
curiouser@ccmb.ap.nic.in



---


From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 13:49:17 2000
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From: "M. Scherf" <scherf@gsf.de>
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Subject: Re: sequence analysis of 5'UTR - HELP
Date: Fri, 07 Apr 2000 14:21:25 +0200
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topalli@my-deja.com wrote:
> 
> Hi,
> 
> I have several kb of the 5' untranslated region of a gene.  Is there any
> software out there that can do some preliminary analysis of this
> sequence for me?  Is there any such resources in the Web.

yes - have a look at

http://genomatix.gsf.de 
 
> Specifically I'd like to look for response elements, transcription factor
> binding sites, TATA, CAAT boxes and the like.  It seems like a pretty
> basic problem and a fairly mechanical process so I would be surprised if
> there were not publicly available resources.

Transcription factor binding sites can be found with the software
MatInspector. The program is one of several tools which are available 
on the genomatix server:

http://genomatix.gsf.de/cgi-bin/matinspector/matinspector.pl


Matthias

-- 
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Dr. Matthias Scherf          

Tel.:  +49 (89) 3187-4060    GSF Forschungszentrum Umwelt & Gesundheit
Fax.:  +49 (89) 3187-4400    Ingolstaedter Landstr. 1
E-mail:scherf@gsf.de         D-85764 Neuherberg (Germany)    

http://www.gsf.de/biodv, 
http://wwwbrauer.informatik.tu-muenchen.de/~scherf
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/


From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 14:14:55 2000
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"Malay" wrote:
> Under such circumstances I'd appreciate your comments in this
> regard. Which language will be "the language" in Bioinformatics,
> Java or C++?


Yes.  No.

There is no and will be no "the language" for bioinformatics.
There are projects in C, C++, Java, Perl, Python, Tcl and no
doubt even Visual Basic.

Most of the existing code is in C.  It's been around a long time
and is quite portable.  It's old enough that there are no
"BioC" projects - there are 1000s of different projects written
in C.

I prefer a mixed C/C++ and Python solution; the former for the
speed (performance) and the latter for the speed (development).
Take a look at biopython.org for some of the Python work.  I
think Python's a great "real programming language."  There's
also JPython if you want to run Python in a Java environment

Others love Perl's ability to sling strings around.  Take a
look at bioperl.org for examples.  You already say you know
Perl - you *can* do good software engineering in Perl.  Outside
of C/C++, I would say most people in bioinformatics use Perl.

And there are people working on Java.  Best place I know for
code is ... yep, biojava.org .  I've not used Java nor even needed
to compile Java code, so I can't say much about how it's used.

Then there are projects to get the different languages working
together.  One of these is via CORBA (see the Life Science Research
work at www.omg.org for extreme details).  Another is using
XML as the exchange protocol (see bioxml.org).

If you are choosing between C++ and Java, I would suggest C++.
Not wanting to raise flames here, but it's a much more powerful
language compared to Java - so long as you don't treat it as
just a better C.  That is, learn how to use C++ strings, templates
and exceptions, not char *, void * and out-of-range return values.

If you want to look at any of the languages on my list, I would
suggest Python.  For GUI work, there's even wxPython; an interface
to wxWindows, which you mentioned in your post.

                    Andrew
                    dalke@acm.org





From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 14:38:49 2000
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Any spreadsheet program (Excel, Quattro, Lotus) will do this.  For nicer
graphs use SigmaPlot or GraphPad.  Both offer non-linear as well as linear
regression analysis.

As mentioned by another respondent, SPlus will do it too, but is probably
overkill for this application.

Ellis


Kurt Sims wrote:

> Hi
>
> I'm looking for a nice simple program that will let me plot the points
> for a scattergram, give it a best fit line and then read an unknown.  I
> would love to hear some suggestions.
>
> All I need it to do is accept the standards for the X axis and Y axis
> and then give me the reading when I give it an unknown reading off of
> one of the axis.
>
> The program can be either PC or Mac based, or even on the web.
>
> TIA for any suggestions.
>
> Kurt
>
> --
> To reply by email please remove the two spams out of my return address.

--
=============================================================
Ellis Golub                  Phone: (215) 898-4629
Biochemistry Department      FAX:   (215) 898-3695
University of Pennsylvania   ellis@biochem.dental.upenn.edu
School of Dental Medicine
4001 Spruce Street
Philadelphia, PA 19104-6003
==============================================================





From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 14:50:17 2000
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DNATools can be used free of charge -but requires registration after a
four months demo period.

http://www.dnatools.dk

Soeren

Andreas Simm wrote:

> Hello,
> does anybody know a free softeware, which find
> restrictions sites in a DNA sequence?
>
> Thanks
>
> Andreas

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

DNATools sequencing software:
http://www.dnatools.dk




From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 17:39:05 2000
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Subject: Re: ABI data extraction utilities
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References: <8ca7ae$2c0$1@mercury.hgmp.mrc.ac.uk> <38E98FA0.7658DDBF@med.kuleuven.ac.be> <38EB352D.64682EFD@pitt.edu> <38EB475D.B546C7D3@med.kuleuven.ac.be> <8cgcsa$et7$1@ssauraab-i-1.production.compuserve.com>
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Hi:
I also used Chromas, but it was not updated for quite a long time and is a bit 
flaky.  The best program for viewing, printing, and extracting sequences from 
ABI data is the free program GeneStudio LE, available for download at 
http://www.genestudio.com.  GeneStudio LE will also show SCF files.  A simpler 
version without the viewer of chromatograms is also on that site.  It is called 
SeqVerter.

Another free program that will allow to do this (and much more) is BioEdit 
http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html.  I think 
that GeneStudio LE has a much better ABI chromatogram viewer than BioEdit and 
the interface is much more user friendly.

John




In article <8cgcsa$et7$1@ssauraab-i-1.production.compuserve.com>, 
GysdeJongh@compuserve.com says...
>
>"Przemko Tylzanowski" <przemko@med.kuleuven.ac.be
>> wrote in message news:38EB475D.B546C7D3@med.kuleuven.ac.be...
>>I use Chromas (the freeware version) and am very happy with it.
>> The thing is that sometimes I would like to see the raw data 
>>because the ABI sometimes miscalls the bases. Now, our lab 
>>is PC based and the only Mac is with ABI. So it would be 
>>much more convenient to look at the raw data on PC. I have
>>somewhere a hack for it but I thought perhaps someone 
>>managed a program to read not only
>>the processed data but also the real trace.
>>"Richard J. Dudley" wrote:
>>Have you tried Chromas?
>
>>http://www.technelysium.com.au/chromas.html
>>or BioEdit?
>
>>http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html
>
>Hi,
>there is a pc version for chromas which works very nice. 
>It lets you view , edit , save the ABI called bases. If you choose
>"export" in the "file" menue it will save the raw fluorescent data.
>
>Bioedit can do the same ; it will,however, not save the raw flu. data.
>
>I also tried exTRACE of Mark Berres. I found it very usefull as
>it extracts all the data , not only the raw fluorescense.
>(yes Richard , there is a lot more in the ABI file) It works
>perfectly in a dos window as he describes in this thread.
>
>-- 
>Gys
>
>
>
>



From owner-bio-software@hgmp.mrc.ac.uk  Fri Apr  7 22:03:20 2000
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Is there any freely available windows 95 based program that can do some
simple sequence assembly?. Preferably with the possibility to do sequence
edditing with the help of the traces.
If there is no free program available, what would be a cheap alternative
then?

Thanks a lot,
Leo Heijnen
l.heijnen@hccnet.nl




From owner-bio-software@hgmp.mrc.ac.uk  Sat Apr  8 02:29:19 2000
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From: gilbertd@bio.indiana.edu (Don Gilbert)
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Erich,
Take a look in
  ftp://iubio.bio.indiana.edu/molbio/ncbi/
esp. ncbi-nov95.tar.Z  or the older one  ncbitools.tar.Z

I haven't looked to see what is in these lately, but they
may have what you need.

- Don

--
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd@bio.indiana.edu


From owner-bio-software@hgmp.mrc.ac.uk  Sat Apr  8 04:03:19 2000
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Do you have too many projects and limited time? If high level protein
expression is one of your goals, C&P Biotech is ready to help you with
sub-cloning and protein purification in E. coli.

1.        Sub-cloning.
          
PRICE: US$ 600.00 per sample

 
2.  Site-directed mutagenesis, large deletion and
         insertion mutation.

PRICE: US$ 900.00 per sample.

 
3.    Protein expression and purification based on GST or histidine-tag
fusion.

 
PRICE: US$ 1000.00, 5.0 mg electrophoresis pure protein is guaranteed.

Give yourself the chances to concentrate on other important projects
with
knowing that professionals are handling your expression and purification
work.

NO CHARGE IF WE FAILED.

CONTACT ADDRESS:

Sue Han

C&P Biotech

3 Hampton Way

Thornhill, Ontario

Canada, L3T 5C8

Email: suehan@sprint.ca

Tel: 905 886 1898

Fax: 905 886 1898
---


From owner-bio-software@hgmp.mrc.ac.uk  Sat Apr  8 05:01:55 2000
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From: Markus Hoenicka <hoenicka_markus@compuserve.com>
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Subject: Re: searching for restriction sites
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Try tacg, a free and extremely powerful tool which is available
for many platforms.

Overview:
http://24.1.175.29/tacg3

Unix sources and some binaries:
http://24.1.175.29/tacg/dist/

A www interface:
http://24.1.175.29/tacg/

A Win32 port (using the CygWin tools):
http://members.tripod.com/~mhoenicka/tacg.html

regards,
Markus

Andreas Simm <simm@klin-biochem.uni-wuerzburg.de> writes:

> Hello,
> does anybody know a free softeware, which find
> restrictions sites in a DNA sequence?
> 
> Thanks
> 
> Andreas
> 
> 

-- 
Markus Hoenicka
hoenicka_markus@compuserve.com
http://ourworld.compuserve.com/homepages/hoenicka_markus/


From owner-bio-software@hgmp.mrc.ac.uk  Sat Apr  8 11:50:50 2000
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Date: Sat, 8 Apr 2000 18:36:28 +0800 
Message-ID: <38eefcbf.1563139@news.ex.nus.edu.sg>
From: gmsia@yahoo.com
Subject: Re: Java or C++
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I was faced with the same choice one year ago. I came down on the side
of C++ after dabbling for a while with Java. At the risk of inviting
flames, I'll talk a bit about my reasoning a year ago.

Java is frequently touted as being platform independent. I regard this
as biased advertising. Java is itself a platform, and there are still
many computers in the world that does not come with JRE, and insisting
that users download JRE is a somewhat draconian approach. Even
assuming that in future, all major OSes will come bundled with JRE,
Java is STILL not platform independent. It is possible to write code
in Java that will break in some OSes but not others. In fairness, this
is not the fault of Java ... it is simply not possible to get the same
code to run on OSes with very big differences in their systems- and
events-handling philosophy. To remedy this, Sun came out with Java
Foundation Classes, which further insulates the programmer from the
system, with another hit to performance. However, analogous class
libraries also exist in the C++ world, such as wxWindows. So on closer
look, C++ can also claim to be "platform-independent" if it is
complemented by class libraries.

Another advantage of Java is that it has a very complete set of
libraries. This is very true, and is indeed very convenient for
programmers. However, C++ also has many free libraries. They just
don't come nicely packaged. In addition, without an "official"
library, many different libraries have developed, which offers
programmers a choice. You might also want to check out V-GUI. It has
less features than wxWindows, but is sufficient for most purposes, and
is far easier to learn.

Lastly, Java is also said to be a modern language. Having learnt from
the mistakes of C++, it has abolished many C++ features that tend to
cause bugs (e.g. pointer arithmetic), has a cleaner object-oriented
programming interface, and has robust runtime garbage collection to
prevent memory leaks. The above claims are true for mediocre
programmers in C++ who have taken an incorrect approach to C++, i.e.
as an extension of C. Problems with memory leaks and pointer
arithmetic arose in C, and C++ was designed to PREVENT these
situations. There are classes in the STL of C++ which implements
bounds-checked arrays etc.

I like C++ because

1) It is flexible. Java adheres strictly to OOP, C++ is both
procedural and OO. Java has a "cleaner" OOP interface because it has
eliminated some of the more obscure and infrequently used features in
C++. However, I take the position that just because a feature is there
doesn't mean that you have to use it. And in the unlikely event that I
DO need to use some obscure feature, I have the option of doing so in
C++. (The major problem of being flexible, of course, is that it makes
C++ an immensely complicated langauge.)

2) C++ gives one a better education. A complete education in C++ will
include C, and a good education in C gives one greater insight into
machine language and systems level programming.

To conclude, it is my personal opinion that if you're in this for the
long haul, C++ is a better investment of time. Personally, I use Perl
for rapid prototyping, and C++ when there are routines which are
memory and time intensive.











From owner-bio-software@hgmp.mrc.ac.uk  Sat Apr  8 21:15:39 2000
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From: greg@franklin.burnham-inst.org (Dr. Greg Quinn)
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Subject: Re: Java or C++
Date: 8 Apr 2000 20:22:48 GMT
Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE
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Both.
It will help you get used to the idea of quickly taking on new languages, 
which you'll have to do in your career as a programmer. 

Malay (curiouser@ccmb.ap.nic.in) wrote:
: Dear Gurus:
: 
: I am a Ph.D. student in Molecular Biology and have a plan to persue a career
: in Bioinformatics. I have a strong background in Javascript/html and I am
: quite comfortable with C and Perl. I want to learn a "real programming
: language" and not being able to choose between Java and C++. On one hand
: Java has the advantage of being platform-independent and writing a GUI based
: program in Java is very easy. On the flip side Java is extremely slow and
: migration into system level programming is almost impossible. On the other
: hand, C++ will be an eternal language and particularly with increasing
: popularity of Linux will be an important language in the days to come and
: writing elementary GUI with platform independent toolkits like wxWindows are
: not very difficult.
: 
: Under such circumstances I'd appreciate your comments in this regard. Which
: language will be "the language" in Bioinformatics, Java or C++?
: 
: Thank to you all who will help in shaping up my career!
: 
: Malay
: 
: Malay Kumar Basu
: Centre for Cellular and Molecular Biology
: Hyderabad 500007
: I N D I A
: 
: Fax: (00-91)40-7171195
: Phone: (00-91)40-7172241
: -----
: Cataholic: Can't stop bringing cats home.
: -----
: curiouser@ccmb.ap.nic.in
: 
: 
: 
: ---

-- 
*****************************************
Computational Biology Group
The Burnham Institute
(formerly La Jolla Cancer Research Inst.)
10901 North Torrey Pines road
La Jolla
CA92037
 
Phone:(619) 646 3103
Email: greg@franklin.ljcrf.edu
http://franklin.ljcrf.edu/greg
http://www.greg.com/
*****************************************


From owner-bio-software@hgmp.mrc.ac.uk  Sat Apr  8 21:31:58 2000
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From: vlad@im.net.ua ("Vlad Belov")
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Hello. We thought you could be interested... We have hundreds of programs and 
games for sale. Very cheap. Please go to : 
http://www.im.net.ua/users/bvi-soft/  
or
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And it is not copied on CD-Rs.

thank you very much.
Vlad
vlad@im.net.ua

---


From owner-bio-software@hgmp.mrc.ac.uk  Sun Apr  9 01:58:54 2000
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Dr. Greg Quinn wrote:
> Both.
> It will help you get used to the idea of quickly taking on new
> languages,  which you'll have to do in your career as a programmer.

But if that's the point, C++ and Java are too close together to
get an idea of the spectrum of languages available.  Other ones
could be Scheme, Smalltalk, Eiffel and Haskell - each with their
own, different views of the world.  Hmm, and toss in Forth, an
APL derivitive like J, and Prolog, and you'll cover most of the
major categories :)

I should point out that of these languages, I've only heard of
people using Smalltalk for bioinformatics software.

                    Andrew
                    dalke@acm.org





From owner-bio-software@hgmp.mrc.ac.uk  Sun Apr  9 09:12:08 2000
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In article <87em8hjl28.fsf@SCHORSCH.MININET>, Markus Hoenicka
<hoenicka_markus@compuserve.com> wrote:

> Try tacg, a free and extremely powerful tool which is available
> for many platforms.
> 
> Overview:
> http://24.1.175.29/tacg3
> 
> Unix sources and some binaries:
> http://24.1.175.29/tacg/dist/
> 
> A www interface:
> http://24.1.175.29/tacg/
> 
> A Win32 port (using the CygWin tools):
> http://members.tripod.com/~mhoenicka/tacg.html
> 
> regards,
> Markus

And instructions for compiling it for plain old DOS are
available at;
   http://itsa.ucsf.edu/~bpm/tacg.html

(I can upload a pre-compiled binary if anyone needs it)

 
> Andreas Simm <simm@klin-biochem.uni-wuerzburg.de> writes:
> > does anybody know a free softeware, which find
> > restrictions sites in a DNA sequence?


   Bernard

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


From owner-bio-software@hgmp.mrc.ac.uk  Sun Apr  9 13:08:55 2000
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> Dr. Greg Quinn wrote:
> > Both.
> > It will help you get used to the idea of quickly taking on new
> > languages,  which you'll have to do in your career as a programmer.
>

I beg to differ. This attitude has created lot of problems for  me atleast.
Each of this languages is a midset by itself and sometimes can be a lifetime
affair by itself. Sure, knowing many languages help in computer as well as
in real life but writing a piece of art will require mastery over a
particular language. Like I said one life is not enough to learn a language
like "C".

> But if that's the point, C++ and Java are too close together to
> get an idea of the spectrum of languages available.

Not very close. Syntax wise may be. But structure wise completely different.
And each one require a different approach to solve a problem.

>Other ones
> could be Scheme, Smalltalk, Eiffel and Haskell - each with their
> own, different views of the world.  Hmm, and toss in Forth, an
> APL derivitive like J, and Prolog, and you'll cover most of the
> major categories :)

Goshh!!!!!! I want to be immortal...

Malay


---


From owner-bio-software@hgmp.mrc.ac.uk  Sun Apr  9 14:03:57 2000
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Malay wrote:
> I beg to differ [with Dr. Quinn's statement]. This attitude has
> created lot of problems for me at least.  Each of this languages
> is a midset by itself and sometimes can be a lifetime affair by
> itself.

My reply to his point was that if the answer is to learn both C++
and Java because "It will help you get used to the idea of quickly
taking on new languages", then it would be better to learn only one
of those two *and* another language which is more dissimilar.

> Like I said one life is not enough to learn a language
> like "C".

Of the language I listed, I think C++ is the hardest.  I think
it takes a good couple years to be good with it, and about 4-5
years to work out some of the subtle parts.  The "lifetime" is
only needed to understand some of the truely deep and complex
issues, which rarely come up in real life.

Something like Python only takes a couple of months to understand
well, though there are still a couple of new areas for me after
two years.

I said:
>> But if that's the point, C++ and Java are too close together to
>> get an idea of the spectrum of languages available.

You replied:
> Not very close. Syntax wise may be. But structure wise completely
> different.
> And each one require a different approach to solve a problem.


I'm going to have to disagree with you here.  Java is a lot
closer to C++ than to any of the other languages I mentioned (Perl,
Python, Scheme, Smalltalk, Eiffel, Haskell, Forth, APL, J, or
Prolog).  Compared to the last few languages, C++ and Java might as
well be the same language, since it's relatively easy to write
Java-like code in C++, but I can't even imagine how to write
Java-like code in Prolog.

My point is that without learning at least a bit of why other
languages exists, it's hard to judge how similar or dissimilar
C++ is from Java.

Oh, and probably Eiffel is next closest language to Java, followed
by Perl or Python.  Eiffel has a different view of how to deal
with types, introduces the concept of pre- and post-conditions,
and does exceptions and multithreading in ways that aren't quite
the way I like them, but at least it's statically typed.  The two
P languages are both dynamically typed, and by capability rather
than class.

>Goshh!!!!!! I want to be immortal...

Nahh, you don't have to be *good* in all those languages; just
know what they're about.  Eg, I've only read through the Eiffel
and Smalltalk books, and some of the commentaries about them.
I've done enough with APL to like it and realize why I'll never
use it for anything, and the same with FORTH.

Besides, I ended up saying:
> I should point out that of these languages, I've only heard of
> people using Smalltalk for bioinformatics software.

which suggests that if you wanted to "get used to the idea of
quickly taking on new languages" and still be realistic about
being able to use those languages, then when combined with my
original answer means you should learn C++ and Smalltalk.

Though I really recommend C++ and Python, and skipping Java.

                    Andrew
                    dalke@acm.org






From owner-bio-software@hgmp.mrc.ac.uk  Sun Apr  9 16:26:37 2000
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Malay wrote:

> Dear Gurus:
>
> I am a Ph.D. student in Molecular Biology and have a plan to persue a career
> in Bioinformatics. I have a strong background in Javascript/html and I am
> quite comfortable with C and Perl. I want to learn a "real programming
> language" and not being able to choose between Java and C++. On one hand
> Java has the advantage of being platform-independent and writing a GUI based
> program in Java is very easy. On the flip side Java is extremely slow and
> migration into system level programming is almost impossible. On the other
> hand, C++ will be an eternal language and particularly with increasing
> popularity of Linux will be an important language in the days to come and
> writing elementary GUI with platform independent toolkits like wxWindows are
> not very difficult.

I'll suggest to use both.
C/C++ for the algorithmics, so you get speed and also portability, at this
level,
Java for interfaces and networks, so you can easy deal with such things, in a
portable way.
I'm not inside bionformatics... just informatic, but I think that would be a
god choice (of course you can use both togehther).
If you think it's a problem larning both,
then think that for fast algorithms you will probably use C++ just as C alone,
and using Java will not bother you with learning some platform-specific
toolkit, so I think finally you'll save time.
Of course I'm tolking of "real" programming, probably there are some easier
solutions around.

Andrea



From owner-bio-software@hgmp.mrc.ac.uk  Mon Apr 10 06:20:11 2000
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Ellis Golub wrote:
> 
> Any spreadsheet program (Excel, Quattro, Lotus) will do this.  For nicer
> graphs use SigmaPlot or GraphPad.  Both offer non-linear as well as linear
> regression analysis.
> 
> As mentioned by another respondent, SPlus will do it too, but is probably
> overkill for this application.
> 
I agree (it was me who suggested this). I did not express myself
clearly, but my intention was to say that *any* decent program will do,
and you probably have one already and so you do not need to get anything
new. I just took the one closest to my fingers, and I could not force
myself to say that you can probably use even Ex*l.

cheer,s jo
-- 
J.Oksanen -- UHLA (University of Helsinki at Lahti)


From owner-bio-software@hgmp.mrc.ac.uk  Mon Apr 10 06:20:13 2000
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From: Jari Oksanen <jari.oksanen@helsinki.fi>
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Malay wrote:
> 
> Dear Gurus:
> 
> I am a Ph.D. student in Molecular Biology and have a plan to persue a career
> in Bioinformatics. I have a strong background in Javascript/html and I am
> quite comfortable with C and Perl. I want to learn a "real programming
> language" and not being able to choose between Java and C++. 

You are comfortable with C and perl and you still want to learn
something else! Why? Why not just deepen your knowledge in perl and C
and you will outsmart anybody trying to do the same in C++ or Java (at
least in terms of time used in programming, the speed of your programs,
the size of your code, the efficiency of resource use, and the power of
your programs). If you just want to add OO, you can have that in perl
now -- or then you can migrate from perl to Python and keep C in any
case.

cheers, jo
-- 
J.Oksanen -- UHLA (University of Helsinki at Lahti)
C-h i m emacs RET m text RET m formatted RET
"GNU Emacs is evil." Linus Torvalds


From owner-bio-software@hgmp.mrc.ac.uk  Mon Apr 10 13:12:34 2000
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From: Normand <normjol@moncourrier.com>
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Does anyone know if there's a freeware running on Windows to analyze 2D
protein gel ? I would like to compare two gels for new or different
proteins. I already found ScionImage, but this software is unable to do
this kind of job. I also found a web site that does this knid of
analysis (NCI Flicker), but I would prefer a software running localy on
my computer.

Thank you.



From owner-bio-software@hgmp.mrc.ac.uk  Mon Apr 10 13:34:38 2000
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From: letondal@nefertiti.pasteur.fr (Catherine  Letondal)
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Subject: Re: image analysis software
Date: 10 Apr 2000 16:33:57 GMT
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In article <38F1C544.2B6F1BB@moncourrier.com>, Normand <normjol@moncourrier.com> writes:
>Does anyone know if there's a freeware running on Windows to analyze 2D
>protein gel ? I would like to compare two gels for new or different
>proteins. I already found ScionImage, but this software is unable to do
>this kind of job. I also found a web site that does this knid of
>analysis (NCI Flicker), but I would prefer a software running localy on
>my computer.
>
>Thank you.
>
>

You may try this:
http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?query=image&exact_word=1&english=1

-- 
Catherine Letondal -- Pasteur Institute Computing Center


From owner-bio-software@hgmp.mrc.ac.uk  Mon Apr 10 14:23:28 2000
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From: Kevin Howe <klh@sanger.ac.uk>
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Subject: ANNOUNCING PFAM RELEASE 5.2
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                ANNOUNCING PFAM RELEASE 5.2
                ===========================


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 5.2 contains 2128 families.  65% of proteins in SWISSPROT 38
and TrEMBL 11 have at least one match to a Pfam family.


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/
               ftp://ftp.cgr.ki.se/pub/data/Pfam/

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

and also the Wise2 software, available from

               http://www.sanger.ac.uk/Software/Wise2/

___________________
The Pfam consortium
00-04




From owner-bio-software@hgmp.mrc.ac.uk  Mon Apr 10 17:50:34 2000
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