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Practical Innovation at BioCon 2003


Blastology and Open Source: Needs and Deeds
Iddo Friedberg, The Burnham Institute

Track: Bioinformatics.Org
Date: Wednesday, February 05
Time: 1:30pm - 2:15pm
Location: Plaza

PSI-BLAST is by far the single most frequently used bioinformatic tool. PSI-BLAST is being used for such diverse purposes as location of distant homologs, fold prediction, evolutionary analysis, sequence annotation, function assignment, and more. PSI-BLAST also serves as the gold standard for comparison with other tools. A computational biologist dealing with protein sequences and/or structures will eventually run it, and will need her own software tools to analyze the plethora of data output.

In his talk, Friedberg goes through a relatively simple PSI-BLAST-based tool, PeCoP, to review the following:

1) PSI-BLAST 101: what it does and how it does it.

2) PSI-BLAST based analysis tools, online and standalone.

3) Output analysis, parsing, and beyond. Special emphasis on NCBI- and Bio*.Org-provided tools.

4) Existing infrastructure, and what do we still need?

Friedberg adds, “The initial title for this presentation was ‘PSI-BLAST: beyond distant homologies.’ You can see why I scrapped it, but the gist is there: with the aid of several simple modules, PSI-BLAST can be transformed from a powerful distant homology searching tool to a profile building tool, a tree building tool, a fold prediction tool, etc. My aim is that, after my presentation, attendees will have knowledge of available tools and implementations for post-PSI-BLAST processing. Hopefully, some will start coding up those modules which are missing.”

Download presentation file

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