A complex approach to recognize 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 no method optimal for all kinds of sites occurs among the considered methods, so in each case, the appropriate way of recognition should be chosen. The approach proposed allows one to minimize the errors of 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.
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