From stephenhuo at yahoo.com  Mon Aug 11 07:01:12 2003
From: stephenhuo at yahoo.com (yongyang huo)
Date: Mon Aug 11 14:01:29 2003
Subject: [Discuss] where can i find the dataset?
Message-ID: <20030811130112.29992.qmail@web20714.mail.yahoo.com>

Dear Group members:
  HI, i am a postgraduate student from University of Ulster, Northern Ireland; my name is 
Stephen Huo. As i am doing a Msc dissertation about prediction of protein secondary 
structure, and therefore i kept searching the proper dataset which contain the sequence of 
amino acids and it's corresponding classification, which may contain the information as 
below:
             classifcation          : CCCCCCCEEEECCCCCCHHC
    sequence of Amino Acids: ACDEFGHIKLMNPQRSTVWY
(H=helix, E=strand, C=coil)
could you tell me where can i found such data? or did The Barton Group contain such dataset, 
if it's all right, could you send me to my email, thank you. And could you also send me the 
set of 496 nonhomologous domains? my email is:
huo-yy@ulster.ac.uk
Thank you very much!
   Best Regards!
Stephen


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From geoff at compbio.dundee.ac.uk  Mon Aug 11 15:29:42 2003
From: geoff at compbio.dundee.ac.uk (Geoff Barton)
Date: Mon Aug 11 14:29:22 2003
Subject: [Discuss] where can i find the dataset?
In-Reply-To: <20030811130112.29992.qmail@web20714.mail.yahoo.com>
References: <20030811130112.29992.qmail@web20714.mail.yahoo.com>
Message-ID: <Pine.WNT.4.55.0308111418060.1404@louse.compbio.dundee.ac.uk>


Stephen,

Thanks for your question, please look at:
http://www.compbio.dundee.ac.uk/~www-jpred/data/ for data sets related to
protein structure prediction studies.

I'm not sure exactly what you are looking for regarding:

>              classifcation          : CCCCCCCEEEECCCCCCHHC
>     sequence of Amino Acids: ACDEFGHIKLMNPQRSTVWY
> (H=helix, E=strand, C=coil)
> could you tell me where can i found such data? or did The Barton Group contain such dataset,
> if it's all right, could you send me to my email, thank you. And could you also send me the

but you need to look at the two research papers published by Cuff and
Barton to see the appropriate references to the literature.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10081963&dopt=Abstract
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10861942&dopt=Abstract

If you can't get these papers from your library, write me an email
directly and I will send you pdf files.

I hope this helps,

Geoff.

------------------
Geoff Barton, Professor of Bioinformatics,   School of Life Sciences
University of Dundee, Scotland, UK.       geoff@compbio.dundee.ac.uk
Tel:+44 1382 345860/345843 (Fax:345764)     www.compbio.dundee.ac.uk
From andresl at iastate.edu  Thu Aug 21 20:12:17 2003
From: andresl at iastate.edu (Andres Lopez)
Date: Wed Oct  1 11:07:13 2003
Subject: [Discuss] Alscript and US letter paper
Message-ID: <9121421710342321@webmail.iastate.edu>


Dear Dr. Barton,

I have been using ALSCRIPT to adjust some output from AMAS so it can be printed
on US letter paper with proper margins.  However, I have not been able to get
the desired results using the X and Y _offset commands.  The commands work fine
with the left and bottom margins, but invariably the block of sequences is
shifted to the right all the way to the page's edge (often cutting part of the
sequence).

I used the max and min _side commands to set the paper size.  I am using version
2.0 of your program.

I would appreciate any suggestions from your experience or from that of users of
your program that use the US letter format.

Thank you in advance,
Andres Lopez.