[Bioperl-l] Newbie bioperl questions

[Peter Schattner]

Arne Elofsson wrote:

> 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
>

Hi Arne

This sounds great.  I would suggest looking at modifying Bppsilite.pm rather
than Bplite since it deals directly with parsing psiblast reports.
Bppsilite doe not currently produce an alignment (object) from the psiblast
report.  If bppsilite were modified so that it also could produce an
alignment I think this would be an significant enhancement.  I would
recommend that the alignment be created as a bioperl "SimpleAlign" object.
If this is a task you might be interested in taking on, I (and I am pretty
sure others in bioperl) would be glad to support you in doing it.

Regards

Peter Schattner