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Nucleic Acids Research Advance Access published online on March 5, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp084
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

COTRASIF: conservation-aided transcription-factor-binding site finder

Bogdan Tokovenko*, Rostyslav Golda, Oleksiy Protas, Maria Obolenskaya and Anna El'skaya

Department of Genetic Information Translation Mechanisms, Institute of Molecular Biology and Genetics, NAS of Ukraine

*To whom correspondence should be addressed. Tel: +38 044 526 11 69; Fax: +38 044 526 07 59; Email: to.bogdan{at}gmail.com

Received July 11, 2008. Revised January 14, 2009. Accepted January 30, 2009.

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/.


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