BDNA Video

General description

The approach for revealing significant conformational and physico-chemical properties of functional sites implemented in the database B-DNA-VIDEO. This database is designed to study the sets of various transcription factor binding sites, providing the evidence that transcription factor binding sites are characterised by specific sets of significant conformational and physico-chemical DNA properties. Each B-DNA-VIDEO entry links to the Web-applet recognising the site, which significant B-DNA features are stored in this entry as the "site recognition programs". The linked entry-applet pairs are compiled within the B-DNA-VIDEO system, which is simultaneously the database and the program tools package applicable immediately for recognising the sites stored in the database.

How to Run the Program

Input the DNA sequence of interest into the field "Input DNA Sequence". For example, the analysis of the human apolipoprotein AII gene sequence, EMBL: X04898; HSAPOA2 (181:360) with experimentally determined HNF1 binding site TRASFAC: R03260 (270:294) is illustrated.

Select one of transcription factor binding sites from the list and denote the strand.

Start the tools processing by clicking the button ‘Scan’. The tools output represents the profile of the Score value. The positive peaks of this profile could pinpoint to the potential site recognized.

Ponomarenko J.V., Ponomarenko M.P., Frolov A.S., Vorobyev D.G., Overton G.C., and Kolchanov N.A., (1999) Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinformatics, V. 15, N. 7/8, P. 654-668.