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From: Michael Witty <mw132@mole.bio.cam.ac.uk>
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Subject: helical wheel
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Dear All,
        I think that helical wheel would be a good program to detect
supercoiling of alpha helices if the angle of 

But then I though - has anyone done this before?  Regards, Mike.

Michael Witty
80 Tennis Court Road
Department of Biochemistry
University of Cambridge
Cambridge CB2 1GA
Great Britain

Room 3.01

mw132@mole.bio.cam.ac.uk

Tel +44(0)1223 333662 Lab
    +44(0)1223 766040 Office

Fax +44(0)1223 766002 Departmental




From owner-info-gcg@hgmp.mrc.ac.uk  Fri Feb  2 16:37:29 2001
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From: Michael Witty <mw132@mole.bio.cam.ac.uk>
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Dear All,
        I think that helical wheel would be a good program to detect
supercoiling of alpha helices if the angle of rotation per residue.

But then I though - has anyone done this before?  Regards, Mike.

Michael Witty
80 Tennis Court Road
Department of Biochemistry
University of Cambridge
Cambridge CB2 1GA
Great Britain

Room 3.01

mw132@mole.bio.cam.ac.uk

Tel +44(0)1223 333662 Lab
    +44(0)1223 766040 Office

Fax +44(0)1223 766002 Departmental




From owner-info-gcg@hgmp.mrc.ac.uk  Mon Feb  5 13:52:42 2001
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From owner-info-gcg@hgmp.mrc.ac.uk  Tue Feb  6 22:08:36 2001
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Disculpar el offtopic, estamos buscando enlaces interesantes para añadir 
a nuestro site, por favor enviarla a traves de nuestra pagina en

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From owner-info-gcg@hgmp.mrc.ac.uk  Wed Feb  7 13:22:26 2001
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From: Mike Challen <mike.challen@talk21.com>
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Subject: PAUP in GCG seqlab
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I am trying to use PAUPsearch with an msf file that contains nucleotide
and 0-1 data.  The 0-1 data encodes significant gap/indel presence or
absence.  This type of file runs OK in PHYLIP analyses but I'm
struggling to get the data into PAUPsearch. The program just crashes
with an 'not a GCG file' type of message.  If I remove the 0-1 data it
runs OK. Any suggestions of how to proceed, please? I don't have access
to PAUP outside of GCG.

thanks
Mike




From owner-info-gcg@hgmp.mrc.ac.uk  Wed Feb  7 14:45:49 2001
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From: stevet@bio.fsu.edu (Steve Thompson)
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Hi Mike -

The 0-1 data is known as "mask" data and needs to be encoded as
such.  This is impossible in msf format but can be done in rsf format.  My
recommendation is to use GCG's SeqLab for the entire analysis and your
problems will go away.  SeqLab does require an X graphics interface, but
it is definitely worth it.  See my Mol Evol workshop tutorial at:

http://bio.fsu.edu/~stevet/MolEvol.pdf

The data files to run the tutorial are available in:

http://bio.fsu.edu/~stevet/Data_Files

				Cheers - Steve
						Steven M. Thompson
				A C T G		stevet@bio.fsu.edu
				  \-/	 http://bio.fsu.edu/~stevet/cv.html
				  /\
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---




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From owner-info-gcg@hgmp.mrc.ac.uk  Fri Feb  9 00:23:04 2001
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From owner-info-gcg@hgmp.mrc.ac.uk  Fri Feb  9 19:40:28 2001
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From: Guy Bottu <gbottu@bigben.vub.ac.be>
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Subject: The mystery of the forbidden names
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	Dear colleagues,

During an exercise session one of our students used seqed to make a
nucleic acid sequence file with name "protein". When he tried to run the
program composition, it took a very long time to run and produced an
output saying that there are O bases. The program translate stalled.

This is strange and a I never noticed it before. It seems that the
programs composition and translate do not accept certain input file
names. Besides "protein" another "forbidden" input file name is "new".

Anyone an explanation for this ?

	Sincerely,
	Guy Bottu




From owner-info-gcg@hgmp.mrc.ac.uk  Sat Feb 10 11:05:02 2001
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From: a_z79@yahoo.com
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Subject: Direct e-mail marketing Svcs..
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---




From owner-info-gcg@hgmp.mrc.ac.uk  Sun Feb 11 09:13:40 2001
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From: nofearoftheIRS@shaddup.co.uk
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<p><FONT face="MS Sans Serif"><p><FONT size=2><p><FONT color="#FF0000"><B> IRS TROUBLES PAST OR PRESENT?</B></FONT><B> <BR><p><BR><p><BR><p>IF you have had troubles with the IRS either past or present <BR><p><p><p><p><p><p><p><p><p><p></BODY></HTML>



---




From owner-info-gcg@hgmp.mrc.ac.uk  Mon Feb 12 13:22:35 2001
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From: Simon Andrews <simon.andrews@bbsrc.ac.uk>
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Subject: Re: The mystery of the forbidden names
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Guy Bottu wrote:
> 
> During an exercise session one of our students used seqed to make a
> nucleic acid sequence file with name "protein". When he tried to run the
> program composition, it took a very long time to run and produced an
> output saying that there are O bases. The program translate stalled.

We don't get the same effect on our system (GCG 10.1 DEC-unix).  Seqed
will happily create a nucleotide sequence called protein, and
composition reads it fine (new also works).  Did you check whether the
student had entered any unusual characters into the sequence.  What was
the sequence type written into the sequence header?

An effect we have seen which produces the sort of output you describe,
is when the user is running out of disk quota (either on their account
or on any temporary space which may be being used).  This often results
in 0 size files.  You may be seeing an artifact of this??

TTFN

Simon.




From owner-info-gcg@hgmp.mrc.ac.uk  Mon Feb 12 15:48:30 2001
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From: technoz@fsmail.net
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Subject: You gotta check out these hilarious video clips!
Date: 12 Feb 2001 15:48:11 -0000
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML>
<HEAD><META content="MSHTML 5.50.4611.1300" name=GENERATOR></HEAD>
<BODY bgColor=#ffffee>
<p><font face="sans-serif" size="2">> -----Original Message-----<br>
  > From: Phil Simms <br>
  > Sent: Tuesday, February 9, 2001 4:14 PM<br>
  > To: Barry Sanders <br>
  > Cc: Steve Hartman, Rhonda Smalley, Jimmy Ward, Big Dave, Dean 
Fletcher<br>
  </font><font face="sans-serif" size="2"><br>
  > Subject: FW: -- 3 New Hilarious Video Clips and some more jokes.<br>
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<P><h3>> Five Bucks -</h3>
<p><font face="sans-serif" size="2">> A man is walking around New York with 
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  &gt; As they round the </font><font face="sans-serif" size="2">corner, 
there 
  stands the same hooker. She takes one look <br>
  > at the man and his wife and says, "HA!… see what you get for five 
bucks<i>?</i>"</font> 
  <font face="sans-serif" size="2"><br>
  > </font></p>
<p></P>
<p><font face="Arial, Helvetica, sans-serif">></font><font size="4"><b> My 
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<p><font face="Arial, Helvetica, sans-serif"><font size="2">&gt; "That wife 
of 
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  &gt; </font></font><font face="Arial, Helvetica, sans-serif"><font 
size="2"> 
  next to him in the bar.<br>
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  &gt; </font></font><font face="Arial, Helvetica, sans-serif"><font 
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  &gt; "So?" <br>
  &gt; "So she's a liar… I spent the night with her sister Shirley." 
</font></font><br>
</p>
<p> <b> > *Please Note - to view the video clips you may need to load Windows 
Media Player<br>
  >  from Microsoft.<br>
  &gt; </b></p>
</BODY></HTML>



---




From owner-info-gcg@hgmp.mrc.ac.uk  Mon Feb 12 22:50:39 2001
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Message-ID: <3A886789.10B86254@lionbio.co.uk>
Date: Mon, 12 Feb 2001 22:45:29 +0000
From: Peter Rice <rice@lionbio.co.uk>
Organization: LION Bioscience Ltd
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Subject: Re: The mystery of the forbidden names
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Guy Bottu wrote:
> During an exercise session one of our students used seqed to make a
> nucleic acid sequence file with name "protein". When he tried to run the
> program composition, it took a very long time to run and produced an
> output saying that there are O bases. The program translate stalled.
> 
> This is strange and a I never noticed it before. It seems that the
> programs composition and translate do not accept certain input file
> names. Besides "protein" another "forbidden" input file name is "new".

Yes - both are GCG database names, so if they are used with no extension GCG
will try to use that database instead. NEW was an alias (IIRC) for PIR2 and
PIR3, and PROTEIN was an alias for PIR1,PIR2 and PIR3. On VMS they were
logical names.

Another side effect was that on VMS - it was impossible to have NEW as a
username (it is a common English family name) because VMS would find the
logical name and try to send email to the PIR divisions instead of to the
user.

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice@uk.lionbioscience.com +44 1223 224723




From owner-info-gcg@hgmp.mrc.ac.uk  Tue Feb 13 00:20:01 2001
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From owner-info-gcg@hgmp.mrc.ac.uk  Tue Feb 13 06:52:15 2001
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From: a_z09@yahoo.com
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From owner-info-gcg@hgmp.mrc.ac.uk  Tue Feb 13 18:57:08 2001
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From: tuesday0098@wiredinvestor.com
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Subject: CAN BULK E-MAIL WORK 4 U?  YES!--GET 1 FREE MILLION
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From owner-info-gcg@hgmp.mrc.ac.uk  Tue Feb 13 20:17:25 2001
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Subject: Tired of the 40 X 40 X 40 Plan?                         23427
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From owner-info-gcg@hgmp.mrc.ac.uk  Wed Feb 14 18:41:36 2001
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From: Guy Bottu <gbottu@bigben.vub.ac.be>
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Subject: Re: The mystery of the forbidden names
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Peter Rice <rice@lionbio.co.uk> wrote:

> Yes - both are GCG database names, so if they are used with no extension GCG
> will try to use that database instead. NEW was an alias (IIRC) for PIR2 and
> PIR3, and PROTEIN was an alias for PIR1,PIR2 and PIR3. On VMS they were
> logical names.

Yes, that's it ! If I use "sw" as file name, composition creates an
erroneous result file with name "swissprot.composition". This however must
be considered as a bug, since GCG programs should recognize *:* as a
databank sequence and anything else as a private sequence. And why does
map not have the problem ?

	Guy Bottu




From owner-info-gcg@hgmp.mrc.ac.uk  Fri Feb 16 09:38:55 2001
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$BK|$,0lL5NAL5=$@5$N%"%@%k%H%5%$%H$K6=L#$,$J$$J}$KFO$$$F$7$^(B
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$B%j%9%H:o=|0MMjO"Mm@h!'(Bad@getachance.com

$B!!%3%A%i"*"*(B    http://www.smileforme.net/jack/     $B"+"+%3%A%i(B

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$B!!%3%A%i"*"*(B    http://www.smileforme.net/jack/     $B"+"+%3%A%i(B

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$B%j%9%H:o=|0MMjO"Mm@h!'(Bad@getachance.com



---




From owner-info-gcg@hgmp.mrc.ac.uk  Fri Feb 16 17:07:18 2001
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From: shodan@execs.com (Edward Lawrence)
X-Newsgroups: bionet.software.gcg
Subject: What Do You Think Of This New Software!!!!
Message-ID: <3a8d421b.2529387@news.direct.ca>
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Greetings,

We are in the process of introducing an extremely exciting new piece
of Internet Software to the market in late March 2001. This software
acts as a very unique new Browser, Portal/Post Office, News Reader and
Digital DashBoard. 

We are looking for feedback from the computer community as to your
reaction to this software concept. Please take a look at this
phenomenal new product and let us know what you think!

http://www.alphatrend.com/Itool_News.htm 


Thanks In Advance for your interest............Edward.




From owner-info-gcg@hgmp.mrc.ac.uk  Sat Feb 17 20:55:16 2001
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From: "Biocity" <pablo.mail@terra.es>
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Subject: Biology web - Página web de Biología
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http://biocity.iespana.es

Temas

Bioinformática
Etología
Fisiología Animal
Fisiología del desarrollo
Fisiología Vegetal
Inmunología
Microbiología
Zoología










From owner-info-gcg@hgmp.mrc.ac.uk  Sun Feb 18 05:08:15 2001
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From: homecareer12@spl.at
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Subject: Goodbye To The Morning Commute!!!!
Date: 18 Feb 2001 05:08:08 -0000
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------=_NextPart_000_2576_0000572D.00006F87
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From owner-info-gcg@hgmp.mrc.ac.uk  Sun Feb 18 10:56:25 2001
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From: sandwich88@kehoo.com
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±ý¯Á¨ú¸Ô²Ó¸ê®Æ½Ð¬¢ 0933018563 ¤ý¤ÀªR®v                
©Î¦Ühttp://seedera.com                           




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           ºØ¤lµêÀÀ¹Î¶¤:www.vteam.com.                        

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±ý¯Á¨ú¸Ô²Ó¸ê®Æ½Ð¬¢ 0933018563 ¤ý¤ÀªR®v                 ·N.................    
©Î¦Ühttp://www.seedera.com                           




From owner-info-gcg@hgmp.mrc.ac.uk  Fri Feb 23 11:40:20 2001
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From: rans@infoseek.com
X-Newsgroups: bionet.software.gcg
Subject: GREAT LOOKS MEANS GREAT SKIN: For men and women with sensitive skin!
Date: 23 Feb 2001 11:39:46 -0000
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
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DewDrops is a non-oily facial emollient, which soothes and
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---




From owner-info-gcg@hgmp.mrc.ac.uk  Fri Feb 23 20:18:08 2001
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From: Michael Schmitz <schmitz@biophys.uni-duesseldorf.de>
X-Newsgroups: bionet.software.gcg
Subject: Re: The mystery of the forbidden names
Date: Fri, 23 Feb 2001 21:13:54 +0100
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Guy Bottu wrote:
> 
> Peter Rice <rice@lionbio.co.uk> wrote:
> 
> > Yes - both are GCG database names, so if they are used with no extension GCG
> 
> Yes, that's it ! If I use "sw" as file name, composition creates an
> erroneous result file with name "swissprot.composition". This however must
> be considered as a bug, since GCG programs should recognize *:* as a
> databank sequence and anything else as a private sequence. And why does
> map not have the problem ?

map probably doesn't resolve file names as databases unless it
encounters the ":".
Neither should seqed. Trying to resolve a file name as database make
sense for programs that primarily operate on database sequences. 
But I'm speculating here, I've never seen the source of GCG 10 :-)

	Michael




From owner-info-gcg@hgmp.mrc.ac.uk  Sun Feb 25 14:35:17 2001
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From: wkxzyb@dsafdsgf.com
X-Newsgroups: bionet.software.gcg,alabama.decatur.general,mailing.netbsd.users
Subject: L.EGAL C.A.B.L.E TV DE-S.C.R.A.M.B.L.E.R
Date: 25 Feb 2001 11:59:04 GMT
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From owner-info-gcg@hgmp.mrc.ac.uk  Sun Feb 25 18:35:00 2001
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From: gws@nciaxp.ncifcrf.gov (Gary Smythers)
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Subject: Announcement: GenPept 122.0 available
Date: 25 Feb 2001 18:34:53 -0000
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     This is to announce the availability of release 122.0 of the GenPept(R) 
(GenBank Gene Products) Database.  GenPept is provided in a format similar 
to that formerly distributed by GenBank(R) under the administration of 
Intelligenetics Inc.  This GenPept release IS _NOT_ AN OFFICIAL RELEASE FROM 
THE NCBI-GENBANK, but an attempt to provide a data file format compatible 
with existing software products.  

This data format is suitable as an input data file for the GCG program
genbanktogcg -genpept.  Compatibility with other software has not been tested.

Site:      ftp.ncifcrf.gov

Directory: pub/genpept
Files:     gprel122.txt.Z, gpdat122.seq.Z

Directory: pub/genpept/divisions
Files: gpbct1.seq.Z,  gpbct2.seq.Z,  gpbct3.seq.Z  
       gpest1.seq.Z,  gpest2.seq.Z,  gpest3.seq.Z,  gpest4.seq.Z, 
       gpest5.seq.Z,  gpest6.seq.Z,  gpest7.seq.Z,  gpest8.seq.Z,  
       gpest9.seq.Z,  gpest10.seq.Z, gpest11.seq.Z, gpest12.seq.Z, 
       gpest13.seq.Z, gpest14.seq.Z, gpest15.seq.Z, gpest16.seq.Z, 
       gpest17.seq.Z, gpest18.seq.Z, gpest19.seq.Z, gpest20.seq.Z, 
       gpest21.seq.Z, gpest22.seq.Z, gpest23.seq.Z, gpest24.seq.Z, 
       gpest25.seq.Z, gpest26.seq.Z, gpest27.seq.Z, gpest28.seq.Z, 
       gpest29.seq.Z, gpest30.seq.Z, gpest31.seq.Z, gpest32.seq.Z, 
       gpest33.seq.Z, gpest34.seq.Z, gpest35.seq.Z, gpest36.seq.Z, 
       gpest37.seq.Z, gpest38.seq.Z, gpest39.seq.Z, gpest40.seq.Z,
       gpest41.seq.Z, gpest42.seq.Z, gpest43.seq.Z, gpest44.seq.Z,
       gpest45.seq.Z, gpest46.seq.Z, gpest47.seq.Z, gpest49.seq.Z,
       gpest50.seq.Z, gpest51.seq.Z, gpest52.seq.Z, gpest53.seq.Z,
       gpest54.seq.Z, gpest55.seq.Z, gpest56.seq.Z, gpest57.seq.Z,
       gpest58.seq.Z, gpest59.seq.Z, gpest60.seq.Z, gpest61.seq.Z,
       gpest62.seq.Z, gpest63.seq.Z, gpest64.seq.Z, gpest65.seq.Z,
       gpest66.seq.Z, gpest67.seq.Z, gpest68.seq.Z, gpest69.seq.Z,
       gpest70.seq.Z, gpest71.seq.Z, gpest72.seq.Z, gpest73.seq.Z,
       gpest74.seq.Z, gpest75.seq.Z, gpest76.seq.Z, gpest77.seq.Z,
       gpest78.seq.Z, gpest79.seq.Z, gpest80.seq.Z, gpest81.seq.Z,
       gpest82.seq.Z, gpest83.seq.Z, gpest84.seq.Z, gpest85.seq.Z,
       gpest86.seq.Z, gpest87.seq.Z, gpest88.seq.Z, gpest89.seq.Z,
       gpest90.seq.Z, gpest91.seq.Z, gpest92.seq.Z, gpest93.seq.Z,
       gpest94.seq.Z, gpest95.seq.Z, gpest96.seq.Z, gpest97.seq.Z,
       gpest98.seq.Z, gpest99.seq.Z, gpest100.seq.Z, gpest101.seq.Z,
       gpest102.seq.Z, gpest103.seq.Z, gpest104.seq.Z, gpest105.seq.Z,
       gpest106.seq.Z, 
       gpgss1.seq.Z,  gpgss2.seq.Z,  gpgss3.seq.Z,  gpgss4.seq.Z, 
       gpgss4.seq.Z,  gpgss6.seq.Z,  gpgss7.seq.Z,  gpgss8.seq.Z,  
       gpgss9.seq.Z,  gpgss10.seq.Z, gpgss11.seq.Z, gpgss12.seq.Z,
       gpgss13.seq.Z, gpgss14.seq.Z, gpgss15.seq.Z, gpgss16.seq.Z,
       gpgss17.seq.Z, gpgss18.seq.Z, gpgss19.seq.Z, gpgss20.seq.Z,
       gpgss21.seq.Z, gpgss22.seq.Z, gpgss23.seq.Z, gpgss24.seq.Z,
       gpgss25.seq.Z, gpgss26.seq.Z, gpgss27.seq.Z, gpgss28.seq.Z,
       gpgss29.seq.Z, gpgss30.seq.Z, gpgss31.seq.Z, gpgss32.seq.Z,
       gpgss33.seq.Z, gpgss34.seq.Z,
       gphtg1.seq.Z,  gphtg2.seq.Z,  gphtg3.seq.Z,  gphtg4.seq.Z,
       gphtg5.seq.Z,  gphtg6.seq.Z,  gphtg7.seq.Z,  gphtg8.seq.Z,
       gphtg9.seq.Z,  gphtg10.seq.Z, gphtg11.seq.Z, gphtg12.seq.Z,
       gphtg13.seq.Z, gphtg14.seq.Z, gphtg15.seq.Z, gphtg16.seq.Z,
       gphtg17.seq.Z, gphtg18.seq.Z, gphtg19.seq.Z, gphtg20.seq.Z,
       gphtg21.seq.Z, gphtg22.seq.Z, gphtg23.seq.Z, gphtg24.seq.Z,
       gphtg25.seq.Z,
       gpinv1.seq.Z,  gpinv2.seq.Z,  gpinv3.seq.Z,
       gpmam.seq.Z,   gppat1.seq.Z,  gppat2.seq.Z,  gpphg.seq.Z,   
       gppln1.seq.Z,  gppln2.seq.Z,  gppln3.seq.Z,  gppln4.seq.Z,
       gppri1.seq.Z,  gppri2.seq.Z,  gppri3.seq.Z,  gppri4.seq.Z,
       gppri5.seq.Z,  gppri6.seq.Z,  gppri7.seq.Z,  gppri8.seq.Z,
       gppri9.seq.Z,
       gprod1.seq.Z,  gprod2.seq.Z,
       gpsts1.seq.Z,  gpsts2.seq.Z,  gpsts3.seq.Z,  gpsyn.seq.Z,
       gpuna.seq.Z,   gpvrl1.seq.Z,  gpvrl2.seq.Z,  gpvrt.seq.Z

Directory: pub/genpept/updates  (daily, cumulative)
Files:     gpseq_updates.dat.Z

Rel. Date: 25-Feb-2001

Ftp mirror sites have been provided through the kind generosity of the 
following institutions:

   C.D. Nager (nager@fmi.ch), at the Freidrich Miescher Institute maintains:

   Name:       ftp.ecbi.org
   Address:    147.167.128.40
   Directory:  ncifcrf

   Dr Jaime Prilusky (lsprilus@weizmann.weizmann.ac.il), at the Weizmann 
   Institute of Science maintains:

   Name:       bioinformatics.weizmann.ac.il
   Address:    132.76.55.12
   Directory:  /pub/databases/genpept 

We greatly appreciate their efforts in creating multiple points of access, and
reducing the load on our systems.

If you have questions or comments concerning this data, or you experience any
difficulty in downloading the data via ftp, please contact:

Gary Smythers  gws@ncifcrf.gov  301-846-5778
  or
Bob Stephens  bobs@ncifcrf.gov  301-846-5787

# ---------------------------------------------------------------------
# | Gary W. Smythers                      | Internet: gws@ncifcrf.gov |
# | Scientific Applications Analyst       |                           |
# | Advanced Biomedical Computing Center  | Phone:  (301) 846-5778    |
# | SAIC                                  | FAX:    (301) 846-5762    |
# | NCI-FCRDC                             |                           |
# | PO Box B, Bldg 430                    |                           |
# | Frederick, MD 21702-1201   USA        |                           |
# ---------------------------------------------------------------------
===============================================================================
GenPept (R) and GenBank (R) are registered trademarks of the U.S. Department of 
Health and Human Services for the GenBank Gene Products and the GenBank Genetic
Sequence Data Banks.


---




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ªÑ¥«°]¸g·j¯Á¯¸
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http://biocity.iespana.es

Temas

Bioinformática
Etología
Fisiología Animal
Fisiología del desarrollo
Fisiología Vegetal
Inmunología
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From owner-info-gcg@hgmp.mrc.ac.uk  Tue Feb 27 22:13:01 2001
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From: mathog@seqaxp.bio.caltech.edu (David Mathog)
X-Newsgroups: bionet.software.gcg
Subject: GCG current version feedback
Date: 27 Feb 2001 22:12:40 GMT
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This newsgroup has been very quiet for a long time - are people not using
GCG anymore, or is there just nothing to talk about since they took the
code base out of the distribution? 

We've been running 8.1 for years and are considering "upgrading" to the
current version, primarily to obtain access to SeqWeb and SeqLab.  It isn't 
entirely clear that we'll do this, because near as I can remarkably little
else has been added to the package since 8.1 that isn't also available for
free, with source code, from the original authors (BLAST 2.x, for
instance.)  Plus going to the current version means giving up our custom
GCG based code, our custom driver level modifications, and the expanded 500
Kb sequence size limit. 

So a bit of feedback is requested. 

1.  What's it like dealing with GCG these days?  
2.  How is the turnaround time on maintenance requests (crucial if we go 
       this way since wouldn't be able to maintain it ourselves anymore.) 
3.  Do "naive" users get along ok with SeqWeb or SeqLab, or are they just
      as lost with those interfaces as most now are with the command line?  
4.  Is SeqMerge any better than phred/phrap/consed?  Is it so much better
      that it's worth the price?
5.  What alternatives to GCG, if any, have you adopted?

and just slightly off topic

6.  Would you be happier with the product if you had access to the source 
      code?

Thanks,

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




From owner-info-gcg@hgmp.mrc.ac.uk  Wed Feb 28 10:22:18 2001
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From: Simon Andrews <simon.andrews@bbsrc.ac.uk>
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Subject: Re: GCG current version feedback
Date: Wed, 28 Feb 2001 10:06:40 +0000
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David Mathog wrote:

> We've been running 8.1 for years and are considering "upgrading" to the
> current version, primarily to obtain access to SeqWeb and SeqLab.  

I've certainly found the Seqlab has been a very useful tool (especially
the rsf file format).  We're encouraging all our users to try it - most
students aren't happy just using a command line interface these days.

> It isn't
> entirely clear that we'll do this, because near as I can remarkably little
> else has been added to the package since 8.1 that isn't also available for
> free, with source code, from the original authors (BLAST 2.x, for
> instance.)

The addition I use most (apart from rsf support) was the addition of
Meme and Motifsearch (HMM type fragment searches from unaligned
sequences).  I think these are also available separately, but it's still
nice to have all the programs integrated into one large package.  It's
the ability to integrate between different programs which still makes
GCG so useful.

> Plus going to the current version means giving up our custom
> GCG based code, our custom driver level modifications, and the expanded 500
> Kb sequence size limit.
> 
> So a bit of feedback is requested.
> 
> 1.  What's it like dealing with GCG these days?
> 2.  How is the turnaround time on maintenance requests (crucial if we go
>        this way since wouldn't be able to maintain it ourselves anymore.)

I believe you are still supplied with source code but are not allowed to
use it elsewhere.  You may still be able to do minor bug fixes (I may
well get squished by GCG on this one!).  We've not experienced many
problems - probably due to the fact that most programs in the package
have been around for long enough that bugs have been ironed out!  GCG do
still put out point releases to fix bugs though many months can pass
between releases.

> 3.  Do "naive" users get along ok with SeqWeb or SeqLab, or are they just
>       as lost with those interfaces as most now are with the command line?

Haven't tried SeqWeb.  Seqlab is fine once you've got the idea of how it
thinks, but it's not intuitive for new users.  We find that a days
introductory course to Seqlab will get most people up and running.  It's
nice because it presents all of the programs and options to you so you
don't have to remember as many program names / command line switches. 
The editor and graphical capabilities with rsfs are good too.  On the
down side, it's file handling isn't brilliant.  If people don't tidy up
after themselves (which many don't) they can get their file space into a
right mess.  It also has an unfriendly way of performing analyses on
parts of sequences (you can't specify part of a sequence to use after
you have opened the window for the analysis program). It can also be
frustratingly slow for some simple analyses (probably due to the
overhead of opening the relevant X-windows).

> 4.  Is SeqMerge any better than phred/phrap/consed?  Is it so much better
>       that it's worth the price?

We don't use it - we try to encourage people to use Staden, which is
excellent for this kind of work.

> 5.  What alternatives to GCG, if any, have you adopted?

We are now running EMBOSS alongside GCG
(http://www.uk.embnet.org/Software/EMBOSS/).  It's freeware, source code
is supplied, there are no intrinsic limits on sequence sizes, it accepts
(and writes) a wide variety of file formats.  It's getting towards the
stage where it could be a replacement for command line gcg.  It's was
originally written by the crowd who did the EGCG, who started EMBOSS
when GCG went closed source.  There is a web interface, but no finished
X-interfaces as yet (though a couple are being written).

	http://www.uk.embnet.org/Software/EMBOSS/Interfaces/

 
> and just slightly off topic
> 
> 6.  Would you be happier with the product if you had access to the source
>       code?

Personally, not any more.  EMBOSS gives an open source alternative for C
code to study, and most of the small analysis programs I hack together
tend to be in Perl.  Given the state of the competition I wouldn't be
surprised if GCG were to slowly fade away over the next few years.  The
owners are likely to switch their attention to desktop packages such as
Omega, where the next lot of money will be made.

Just my (personal!!) opinions

Simon.




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From: greg@franklin.burnham-inst.org (Dr. Greg Quinn)
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Subject: Re: GCG current version feedback
Date: 28 Feb 2001 14:34:32 GMT
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David Mathog (mathog@seqaxp.bio.caltech.edu) wrote:
: 1.  What's it like dealing with GCG these days?  

I'm guessing you mean the company rather than the package; I've always found the 
people at the GCG to be very helpful and very responsive; It's one of the
few software places I've dealt with a help desk staffed with people who 
really know what they're talking about, even to the extent of dealing
with GCG admin issues.

: 2.  How is the turnaround time on maintenance requests (crucial if we go 
:        this way since wouldn't be able to maintain it ourselves anymore.) 

Answered above.

: 3.  Do "naive" users get along ok with SeqWeb or SeqLab, or are they just
:       as lost with those interfaces as most now are with the command line?  

We're probably about to take the plunge with SeqWeb here (as soon as version
2 is released), after having used W2H for some years. Martin (Senger) has done
a great job with W2H but I have concerns about whether it's still being actively 
developed (last reported W2H release December 17, 1999). SeqLab tends to be seen
still here as an 'advanced' interface here, since it requires XWindows and some
computing savvy; the days of being able to provide a UNIX command line sequence
analysis package for all (or even most) postdocs at a research facility is long 
gone; most postdocs now are increasingly brought up through doctoral training
using desktop packages such as MacVector, LaserGene, etc. Even persuading people 
to use a web interface can be tough, letalone having to learn UNIX.

: 4.  Is SeqMerge any better than phred/phrap/consed?  Is it so much better
:       that it's worth the price?

We checked into it but the pricing was prohibitive for us, as is GCG Link which 
links database searching with the Omega package. 

: 5.  What alternatives to GCG, if any, have you adopted?

EMBOSS is actively being developed by an excellent group of folks in the scientific
community but is still a ways off from being at the GCG level of functionality. The
nice aspect is that it should integrate with the W2H interface

: 
: and just slightly off topic
: 
: 6.  Would you be happier with the product if you had access to the source 
:       code?

Not really; in retrospect it was amazing that GCG continued to distribute source
code until they did (do you know many other sequence software companys doing that...!);
however I do understand it's changed attitudes in some parts of the scientific 
community towards the package.

My gut feeling about GCG is that it's still a bargain at the academic pricing, 
particularly since there's a lot of support available in the form of tutorials
etc, plus any number of users can access it; this is probably the biggest sticking 
point for purchasing desktop software such as MacVector, LaserGene etc in that they're
so damn expensive. 

Hope this helps
Cheers
G.




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From: gilbertd@bio.indiana.edu (Don Gilbert)
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David,

I believe that GCG does still distribute source code, for a price and
an agreement, as their SDK package.  I haven't tried this option yet.

>6.  Would you be happier with the product if you had access to the source 
>      code?
>
>Thanks,
>
>David Mathog
>mathog@seqaxp.bio.caltech.edu
>Manager, sequence analysis facility, biology division, Caltech 

-- Don

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




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