TFBS

From BioPerl

• Transcription Factor Binding Sites are sites in the genome where transcription factor proteins bind to the genome as part of transcription initiation or repression.

• TFBS [1] is also a package of BioPerl-compatible Perl modules that are used for transcription factor binding site detection and analysis.

Example TFBS usage

• Count or Weight matrix (based on Malcom Cook's post)

#!/usr/bin/perl -w
use strict;
use TFBS::PatternGen::SimplePFM;
my @sequences = <>;
chomp @sequences;
print TFBS::PatternGen::SimplePFM->new(-seq_list=>\@sequences)->pattern->rawprint;

References

1. Lenhard B and Wasserman WW. TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics 2002 Aug; 18(8) 1135-6. pmid:12176838. PubMed HubMed [tfbs]