title: COTRASIF: conservation-aided transcription-factor-binding site finder.
abstract: COTRASIF is a web-based tool for the genome-wide search of evolutionary conserved regulatory regions (transcription factor-binding sites, TFBS) in eukaryotic gene promoters. Predictions are made using either a position-weight matrix search method, or a hidden Markov model search method, depending on the availability of the matrix and actual sequences of the target TFBS. COTRASIF is a fully integrated solution incorporating both a gene promoter database (based on the regular Ensembl genome annotation releases) and both JASPAR and TRANSFAC databases of TFBS matrices. To decrease the false-positives rate an integrated evolutionary conservation filter is available, which allows the selection of only those of the predicted TFBS that are present in the promoters of the related species' orthologous genes. COTRASIF is very easy to use, implements a regularly updated database of promoters and is a powerful solution for genome-wide TFBS searching. COTRASIF is freely available at http://biomed.org.ua/COTRASIF/.
authors.affiliation: Department of Genetic Information Translation Mechanisms, Institute of Molecular Biology and Genetics, NAS of Ukraine. to.bogdan@gmail.com
authors.forename: Bogdan
authors.initials: B
authors.lastname: Tokovenko
authors.forename: Rostyslav
authors.initials: R
authors.lastname: Golda
authors.forename: Oleksiy
authors.initials: O
authors.lastname: Protas
authors.forename: Maria
authors.initials: M
authors.lastname: Obolenskaya
authors.forename: Anna
authors.initials: A
authors.lastname: El'skaya
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D016678:Genome; D020407:Internet; D008390:Markov Chains; D051379:Mice; D011401:Promoter Regions, Genetic; D051381:Rats; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors