TFBS

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  • 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 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

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