[Bioperl-l] PSI-BLAST output processing
Wed, 13 Nov 2002 18:26:53 -0800
Apologies for cross-posting. Please email replies directly to me (firstname.lastname@example.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
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,
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171