Tregwiki:Libraries for Programmers

All the usual Bio*-languages support searches for binding sites:

• BioPerl
• TFBS seesm to be the best library for perl, using PDL makes it pretty quick though probably not as fast as cread with its suffix trees
• BioPython has some redundancy, both its Meme modules and AlignACE-support can parse and scan for matrices (see Biopython-Meme example)
• CREAD searches matrices, compares them, mines chipchip, nice and very fast C++ library
• Sven Rahmanns Perl-Module to calculate matrix quality
• Biojava has a Distribution-class that should probably be called WeightMatrix. One of its example programs is the Gibbs Sampler. (Back in 1993, that was a publication in Science. Today it's an example for a library...)
• TAMO (article) is the best library in Python and probably the library for promotor analysis in general: Classes for motifs, motif-databases, scanning, logo-creating and various scoring methods, with parsers for most well-known motif discovery algorithms are included.