[Bioperl-l] Newbie bioperl questions

Arne Elofsson arne@sbc.su.se
11 May 2001 17:58:41 +0200


Hi

Sorry for bothering you, but before I start hacking BioPerl I would
very much like to have some questions answered.

First some quick background. I want to try to use BioPerl for mapping
sequences to domains (for instance from Pfam and Scop), as well in the
future for all of my work in fold-recognition/homology modeling.
Currently I am using a lot of subroutines based on James Tisdall B.pl
library for doing this type of work. I guess I could spend some time
to get the functionality into BioPerl, however I have to get results
too. Now I am starting a small new project and thought that using
BioPerl could help. However, I have some questions:

1) Is anyone working on the structural objects ? If not I would not
mind doing that. I would not do it in a perfect way first, but
focusing on the parts I need, i.e: (a) getting features such as
secondary structure, residues numbers and C-alpha coordinates into a
(modified) sequence object. (b) Implement a PDB-reading routine. (The
main problem is that in PDB is the sequence not well defined, it can
differ between header and coordinates). I guess this could be done
using 


2) I will need to obtain multiple sequence alignments (and profiles)
from psiblast. I have perl code that does this. I would like to modify
BPlite (and related modules) to include this so that you can call
$sbjct->msa and obtain a \@seq_array

3) Include other (i.e. my own) alignment programs, for instance for
sequence-profile alignments.



Thanks for any information that can help me/save my time. It is
possible that rudimentary implementation already exist, if that is so I
would very much like to start from these.

yours

arne
-- 
------------------------------------------------------------------------
 Arne Elofsson     Stockholm Bioinformatics Center
 Net:      arne@sbc.su.se http://www.sbc.su.se/~arne/
 Tel:+46-8-161553   Stockholm Bioinformatics Center, Stockholm University
 Fax:+46-8-158057   10691 Stockholm, Sweden