Conformational and physicochemical DNA features specific for transcriptionfactor binding sites

Motivation: A reliable recognition of transcription factor binding sites is essential for analysis of regulatory genomic sequences. The experimental d ata make evident an important role of DNA conformational features for site functioning. However Internet-available tools for revealing conformational I and physicochemical DNA features significant for the site functioning and subsequent use of these features for sire recognition have not been develo ped up to now: Results: We suggest an approach for revealing significant conformational an n physicochemical properties of functional sites implemented in the databas e B-DNA-VIDEO. This database is designed to study the sets of various trans cription factor binding sites, providing evidence that transcription factor binning sites are characterized by specific sets of significant conformati onal ann physicochemical DNA properties. For a fixed site, by, using the B- DNA features selected for this site recognition, the C-program recognizing this site may be generated, control tested and stored in the database B-DNA -VIDEO, Each B-DNA - VIDEO entry links to the Web-applet recognizing the si te, whose significant B-DNA features are stored in this entry as the 'site recognition programs'. rile pairwise linked entry-applet pairs are compiled within the B-DNA-VIDEO system, which is simultaneously the database and th e program tools package applicable immediately for recognizing the sites st ored in the database. Indeed this is the novelty! Hence, B-DNA-VIDEO is the Web resource of both 'searching for static data' and 'active computation' type, that is why it was called an 'activated database'. Availability: B-DNA-VIDEO is available at http://wwwmgs.bionet. nsc.ru./sys tems/BDNAvideo/ and the mirror site at http://www.cbil.upenn.edu/mgs/system s/consfreq/. Contact: pon@bionet.nsc.ru.