VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Oct 01 2009 - 04:26:01 CDT

Dear VMD users (Multiseq developers),

I am looking into using multiseq for some alignment projects ...
Multiseq seems a very nice interface, however there are a couple of
issues I would like to discuss.

I am following the steps:
1. Upload a multiple fasta sequence file that corresponds to a list of
pdbids:chainids. The fasta file is downloaded from the PDB.
2. Automatically download for each sequence, the corresponding chain in
the corresponding pdb file
3. Aligning the sequences based on the loaded structures
4. Save the alignment profile
5. Use the profile further

The reason I would like to load the fasta file before the structures is
simple: some structures have missing residues, thus if multiseq reads
the sequence directly from the structural residues, it would load an
incomplete sequence. The problem is that upon loading the fasta file
each sequence gets the name "SEQUENCE" in the multiseq lines. The word
"SEQUENCE" is the last column in the fasta headers downloaded from PDB.
The first column is "PDBID:CHAINID". Now, if I try to automatically
retrieve the pdb chains corresponding to the sequences in the fasta
file, this is currently not possible. I would imagine that if each
loaded sequence would be recorded with the name taken from the first
column of the fasta header, the automatic download of the corresponding
chain in the PDB should be possible.

Of course I know that the fasta files from UNIPROT have the sequence
name on the last column, rather than first.

But maybe it would be useful to follow the convention of the PDB fasta
files ...

Best wishes
Vlad 

-- 
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Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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