THE ARGO_SITES: AN ANALYSIS AND RECOGNITION OF THE TRANSCRIPTION FACTOR BINDING SITES BASED ON SETS OF DEGENERATE OLIGONUCLEOTIDE MOTIFS

Motivation: The transcription factor binding sites (TFBS) are the critical determinants of the assembly and positioning of the basal transcription complex, thereby providing the tissue- and stage-specificity of transcription in the eukaryotic genes. Development of new methods to analyse and recognize the TFDSs are required for clarifying the structural - functional organization of the regulatory regions of the eukaryotic genes and improving our understanding of the mechanisms underlying genetic information expression. Results: Based on the method we previously designed for identifying sets of degenerate oligonucleotide motifs, 17 TFBS samples of eukaryotes were analyzed. For the analyzed samples, sets of significant motifs were built, and the specific features of the nucleotide context at the 5'- and 3'- flanking regions were identified for the sites. The ARGO_Sites program for the recognition of the identified TFBSs on the basis of the identified motifs was developed. Availability: http://wwwmgs.bionet.nsc.ru/mgs/programs/argosites/