The identification of the sequence-dependent DNA features correlating with affinity magnitudes of DNA sites interacting with a protein can pinpoint to molecular event limiting this protein/DNA recognition machinery. The approach is realized in computer system ACTIVITY containing the databases on site activity and on conformational and physical-chemical DNA/RNA parameters. By using the system ACTIVITY, an analysis of some sites was provided and the methods for predicting the site activity were constructed.
1. Input the DNA sequence of interest into the field "Input DNA Sequence". For example, recognition of the promoter of Syrian hamster HMG CoA reductase gene (EMBL AC M15960), the experimental USF site TRANSFAC: R00711 (181; 197) is illustrated.
2. Select one of transcription factor binding sites from the list and denote the strand.
3. 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 point to the potential site recognized.
Ponomarenko J.V., Furman D.P., Frolov A.S., Podkolodny N.L., Orlova G.V., Ponomarenko M.P., Kolchanov N.A., and Sarai A. (2001) ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another Nucleic Acids Res.,V.29. N.1. P. 284-287.