Tregwiki:Libraries for Programmers: Difference between revisions
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* BioPerl | * BioPerl | ||
* Could [http://www.biomedcentral.com/1471-2105/9/11/abstract SeqAn] finally be a usable C++ library for DNA sequence analysis? | |||
* 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 | * 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 | ||
* [http://www.biopython.org BioPython] has some redundancy, both its [http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/MEME/Motif.py?rev=HEAD&cvsroot=biopython&content-type=text/vnd.viewcvs-markup Meme] modules and [http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/AlignAce/?cvsroot=biopython AlignACE]-support can parse and scan for matrices (see [[Biopython-Meme example]]) | * [http://www.biopython.org BioPython] has some redundancy, both its [http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/MEME/Motif.py?rev=HEAD&cvsroot=biopython&content-type=text/vnd.viewcvs-markup Meme] modules and [http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/AlignAce/?cvsroot=biopython AlignACE]-support can parse and scan for matrices (see [[Biopython-Meme example]]) | ||
Revision as of 02:58, 15 January 2008
All the usual Bio*-languages support searches for binding sites:
- BioPerl
- Could SeqAn finally be a usable C++ library for DNA sequence analysis?
- 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.
