Bug#320777: ITP: libtfbs-perl -- [Biology] Library for handling transcription factor binding sites
Package: wnpp
Severity: wishlist
Owner: Steffen Moeller <moeller@pzr.uni-rostock.de>
* Package name : libtfbs-perl
Version : 0.5.0
Upstream Author : Boris Lenhard <Boris.Lenhard@cgb.ki.se>
* URL : http://forkhead.cgb.ki.se/TFBS/
* License : artistic
Description : [Biology] Library for handling transcription factor binding sites
TFBS Perl OO modules implement classes for the representation of objects
encountered in analysis of protein-binding sites in DNA sequences.The
objects defined by TFBS classes include:
* pattern definition objects, currently position specific score
matrices (raw frequency, information content and position weight
matrices)with methods for interconversion between matrix types, sequence
searching with a matrix profile, sequence 'logo' drawing and matrix
manipulation;
* a composite object representing a set of position specific score
matrices, with methods for the identification of motifs within DNA
sequences with the set of profiles from its member matrices;
* methods for searching pairwise alignments for patterns conserved
in both sequences (phylogenetic footprinting) defined for both matrix
profile and composite (matrix set) objects;
* an object representing DNA binding site sequence, and an object
representing sets of DNA binding sequences, with methods and helper
classes to facilitate scanning, filtering and statistical analyses;
* an object representing a pair of DNA binding site sequences, and
an object representing a set of such pairs, for storage, manipulation
and analysis of phylogenetic footprinting searches;
* database interfaces to relational, flat file and WWW database of
position-specifc score matrices, with methods for searching existing
databases, as well as creating new ones containing user-defined
matrices.
* interfaces to matrix pattern generating programs
The modules within the TFBS set are fully integrated and compatible with
Bioperl.
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