Motivation: TFBS is a set of integrated, object-oriented Perl modules for transcription factor binding site detection and analysis. It implements objects representing specificity profile matrices, binding sites and sets thereof, pattern generators, and pattern database interfaces. The modules are interoperable with the BioPerl open source system. Availability and Supplementary Information: The module package with documentation and example scripts are available at http://forkhead.cgb.ki.se/TFBS/ Contact: Boris.Lenhard@cgb.ki.se * To whom correspondence should be addressed.