In article <199609151815.NAA17395 at mimer.scs.uiuc.edu> cole at MIMER.SCS.UIUC.EDU (Ronald N. Cole) writes:
> I am faced with a simple, but labor intensive task. I have a large
> list of pdb files (466 to be exact). I would like to turn this list into a
> list of accession numbers. I then want to do a pileup on all of these
> sequences.
>> Does anyone know of an automated or even semi-automated way of doing
> this? I can write scripts or do any programming necessary. I just want to
> know the best way to approach this.
Clearly a task for SRS.
No, not the lame version in GCG 8.x - you need the real SRS for this.
1. Make a list of PDB entries in a file
2. Use this as a query (@filename) in SRS
3. Link it to SwissProt and (nagically) you have the full set of
sequences you need:
% getz "@filename > SWISSPROT"
I guess what you really want to do is to use PileUp to get the tree of
related sequences, rather than a full alignment - or maybe they really
do align.
Anyway, you can try further tests in SRS, like looking for PROSITE motifs
to see whether your PDB entries share a common motif - then you could
of course just align around that part.
If you have HSSP, you can also look for alignments directly from your PDB
entries.
You can try the bionet.software.srs for more help on SRS.
--
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Peter Rice | Informatics Division,
E-mail: pmr at sanger.ac.uk | The Sanger Centre,
Tel: (44) 1223 494967 | Wellcome Trust Genome Campus,
Fax: (44) 1223 494919 | Hinxton, Cambridge, CB10 1SA,
URL: http://www.sanger.ac.uk/~pmr/ | England
