Comparative analysis of methods recognizing potential transcription factor binding sites

A complex approach to recognition of transcription factor binding sites (TFBS) has been developed, based on four methods: (i) weight matrix, (ii) information content, (iii) multidimensional alignment, and (iv) pairwise alignment with the most similar representative of known sites. It has been shown that none of the methods considered is optimal for all kinds of sites, so in each case the appropriate way of recognition should be chosen. The approach proposed allows one to minimize the errors in TFBS recognition. The program available through the Internet (http://www.sgi.sscc.ru/mgs/programs/multalig/) has been created to search for the potential TFBS in nucleotide sequences set by the user.