TFBS

• 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 tfbs 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 Malcolm 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

<biblio>

1. tfbs pmid=12176838

</biblio>