Search for new binding sites for the transcriptional factor SF-1 by the SITECON method: Experimental verification and analysis of regulatory regions of orthologous genes

165 Recognition of transcriptional factor binding sites in genomic sequences is a promising approach to deciphering the regulatory code of DNA. Today, the methods of recognition of transcriptional factor binding sites based of various principles (consensus, weight matrices, etc.) are known and widely used [1]. However, in most cases, the recognition accuracy of transcriptional factor binding sites is insufficient for analysis of extended genomic sequences [2, 3], which makes it necessary to use additional criteria that allow the percent of false predictions to be decreased [3–5]. In addition, in different situations, the existing methods of recognition of transcriptional factor binding sites may differ significantly with respect to recognition quality even within the same approach (e.g., weight matrixes) [6]. For this reason, development of new approaches to recognizing transcriptional factor binding sites remains a topical problem. Another key problem is determination whether the transcriptional factor binding sites predicted by computer methods are functional in the regulatory regions of different genes in vivo (i.e., in chromosomes in living cells).

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