FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.
FOOTER is a newly developed algorithm that analyzes homologous mammalian promoter sequences in order to identify transcriptional DNA regulatory 'signals'. FOOTER uses prior knowledge about the binding site preferences of the transcription factors (TFs) in the form of position-specific scoring matrices (PSSMs). The PSSM models are generated from known mammalian binding sites from the TRANSFAC database. In a test set of 72 confirmed binding sites (most of them not present in TRANSFAC) of 19 TFs, it exhibited 83% sensitivity and 72% specificity. FOOTER is accessible over the web at http://biodev.hgen.pitt.edu/Footer/.
Corcoran
David L
DL
Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
Feingold
Eleanor
E
Benos
Panayiotis V
PV
D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D018983:DNA Footprinting; D005786:Gene Expression Regulation; D020407:Internet; D008322:Mammals / Q000235:genetics*; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
D014157:Transcription Factors