[Bioperl-l] PSI-BLAST output processing

Iddo Friedberg idoerg@burnham.org
Wed, 13 Nov 2002 18:26:53 -0800

Hi All,

Apologies for cross-posting. Please email replies directly to me (idoerg@burnham.org), I
am not a resident of these lists.

I  would like to know the updated status of the various Bio*.org projects with regards to
PSI-BLAST processing. Could one person (or more) from biojava and bioperl answer the
following questions?  This is for a talk at BioCon 2003.

(BioCorba person: please go directly to question #6).

1) Do you have a PSI-BLAST parser? (OK, silly)

2) Filtering capabilities of the parser (e.g. include only sequences with a certain evalue

3) Does your project have a multiple-sequence alignment class or somesuch?
(if not, skip to 4)
3.1) Can the MSA object be created from the PSI-BLAST parser output (/object instance)?
(Easy / Hard / No)
(a code snippet,  semi-functional, would be _highly_ appreciated, here and in questions of
similar vein).
3.2) Can the MSA be transferred as input to other programs?  (Easy / Hard / No)
3.3) Can you filter sequences from the MSA? What criteria?
3.4) Calculating conservation along an MSA column (Easy / Hard / No)

4) Do you have MSA profile / PSSM class, or somesuch?
(if not, skip to 5)
4.1) Creating a profile from a multiple sequence alignment: (Easy / Hard)
4.2) Filtering: same as 3.3

5) Anything else you might like to tell me about the PSI-BLAST output processing
capabilities of your projects would be grand.

6) (For BioCorba) Does BioCorba have a:
6.1) PSI-BLAST output object?
6.2) multiple sequence alignment object?
6.2) PSSM /profile object?
6.3) Anything else relevant to handling PSI-BLAST output?
6.4) IDL code snippets, if relevant, would be cool.

Many, many thanks in advance,


Iddo Friedberg
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171