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REVIEW: Bioinformatical and Experimental Approaches to Investigation of Transcription Factor Binding Sites in Vertebrate Genes

T. I. Merkulova1,2*, D. Yu. Oshchepkov1,2, E. V. Ignatieva1,2, E. A. Ananko1, V. G. Levitsky1,2, G. V. Vasiliev1, N. V. Klimova1, V. M. Merkulov1, and N. A. Kolchanov1,2

1Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, ul. Akademika Lavrentieva 10, 630090 Novosibirsk, Russia; fax: (3832) 331-278; E-mail: merkti@niboch.nsc.ru

2Novosibirsk State University, ul. Pirogova 2, 630090 Novosibirsk, Russia; fax: (3832) 339-101; E-mail: kol@bionet.nsc.ru

* To whom correspondence should be addressed.

Received May 17, 2007; Revision received July 7, 2007
The development of computer-assisted methods for transcription factor binding sites (TFBS) recognition is necessary for study the DNA regulatory transcription code. There are a great number of experimental methods that enable TFBS identification in genome sequences. The experimental data can be used to elaborate multiple computer approaches to recognition of TFBS, each of which has its own advantages and limitations. A short review of the characteristics of computer methods of TFBS prediction based on various principles is presented. Methods used for experimental monitoring of predicted sites are analyzed. Data concerning DNA regulatory potential and its realization at the chromatin level, obtained using these methods, are discussed along with approaches to recognition of target genes of certain transcription factors in the genome sequences.
KEY WORDS: genome annotation, recognition of transcription factor binding sites, computer and experimental methods, databases, training samples

DOI: 10.1134/S000629790711003X