[Bioperl-l] Newbie bioperl questions

[Hilmar Lapp]

Arne Elofsson wrote:
> 
> Sorry for bothering you, but before I start hacking BioPerl I would

Great that you did! Venturing into structural biology support was
discussed on several occasions, but obviously there wasn't anyone yet
who was bold enough to really take it on (= write code, apart from
emails :-)

> 
> 1) Is anyone working on the structural objects ? If not I would not
> mind doing that.

Cool!

> I would not do it in a perfect way first, but

You know the bioperl rule #1: the one with the working code wins the
argument. In this particular case there isn't even an argument ... :)

> (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
> 
> 

I suspect something got lost here?

> 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

Peter already commented, also about the existence of BPpsilite.pm.

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

Cool!

> 
> Thanks for any information that can help me/save my time. It is

Hm. I probably didn't save any of your time; my intention was more to
encourage you.

	Hilmar
-- 
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Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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