MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes

Background: Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced sensitivity and specificity. Results: We describe the implementation of a search method for putative transcription factor binding sites (TFBSs) based on hidden Markov models built from alignments of known sites. We built 1,079 models of TFBSs using experimentally determined sequence alignments of sites provided by the TRANSFAC and JASPAR databases and used them to scan sequences of the human, mouse, fly, worm and yeast genomes. In several cases tested the method identified correctly experimentally characterized sites, with better specificity and sensitivity than other similar computational methods. Moreover, a large-scale comparison u...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Voichita D. Marinescu, Isaac S. Kohane, Alberto Riva
• Keywords: BMCBI 2005, Regulatory Elements, Search Method, Transcription Factor