Package: wnpp Severity: wishlist Owner: Steffen Moeller <[EMAIL PROTECTED]>
* Package name : libtfbs-perl Version : 0.5.0 Upstream Author : Boris Lenhard <[EMAIL PROTECTED]> * 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. -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
