Tregwiki:Libraries for Programmers

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


 * BioPerl
 * Could SeqAn finally be a usable C++ library for motif sequence analysis? It has some nice algorithms, e.g. suffix trees / ESAs
 * 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.