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Briefings in Bioinformatics Advance Access published online on July 12, 2007
Briefings in Bioinformatics, doi:10.1093/bib/bbm027
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes

Nikolay A. Kolchanov, Tatyana I. Merkulova, Elena V. Ignatieva, Elena A. Ananko, Dmitry Yu. Oshchepkov, Viktor G. Levitsky, Gennady V. Vasiliev, Nataly V. Klimova, Vasily M. Merkulov and T. Charles Hodgman

Corresponding author. Elena A. Ananko, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia. E-mail: eananko{at}bionet.nsc.ru

The recognition of transcription factor binding sites (TFBSs) is the first step on the way to deciphering the DNA regulatory code. There is a large variety of experimental approaches providing information on TFBS location in genomic sequences. Many computational approaches to TFBS recognition based on the experimental data obtained are available, each having its own advantages and shortcomings. This article provides short review of approaches to computational recognition of TFBS in genomic sequences and methods of experimental verification of predicted sites. We also present a case study of the interplay between experimental and theoretical approaches to the successful prediction of Steroidogenic Factor 1 (SF1).

Keywords: Genome annotation, transcription factor binding site recognition, computer-assisted and experimental methods, sequence training-samples

Submitted: March 6, 2007. Received (in revised form): June 7, 2007.


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