TFBS: Perl modules for transcription factor detection and analysis

Boris Lenhard

Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden


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:

   o 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;
   o 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;
   o methods for searching pairwise alignments for patterns conserved in both sequences (phylogenetic
     footprinting) defined for both matrix profile and composite (matrix set) objects;
   o 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;
   o 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;
   o database interfaces to relational, flat file and XML databases of position-specifc score
     matrices, with methods for searching existing databases, as well as creating new ones containing
     user-defined matrices.

The modules within the TFBS set are fully integrated and compatible withBioperl. I will discuss the
design, implementation and potential extensionof the TFBS modules. I will also touch on possible
generalizations of thedesign to facilitate analysis of other types of patterns in biological
sequences.