Chris Mungall > go-perl-0.14 > GO::IO::Blast

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NAME ^

  GO::IO::Blast     - Gene Ontology Blast Reports DEPRECATED

SYNOPSIS ^

DESCRIPTION ^

parses a blast report (must be a a blast that was performed on a seqdb that can with headers that can be mapped to go terms via the go database)

takes the blast hits, and finds the corresponding GO terms (currently it requires the fasta to have "genename:" in header but we should make it configurable)

using the GO terms, a GO::Model::Graph is built, with the blast hits attached according to product<->term links.

Any blast hit H that corresponds to a term T implicitly corresponds to all the terms above T in the DAG; eg a hit to a G-protein coupled receptor is implicitly a hit to a transmembrane receptor.

At every node, all the scores (including implicit scores from hits further down) are combined. Currently we are playing with this as the scording scheme:

log2( 2 ** score1 + 2 ** score2 +.... 2** scoreN)

Hits are only counted once at each node.

  TODO - use bioperl to parse full report if required 
           (currently parses summary)

  TODO - configurable ways to go from fasta header to GO terms

  TODO - different scoring schemes

  TODO - result object

PUBLIC METHODS - Blast ^

FEEDBACK ^

Email cjm@fruitfly.berkeley.edu

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself

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