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Nucleic Acids Research 2005 33(Web Server Issue):W417-W422; doi:10.1093/nar/gki459
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Article

ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters

Oleg V. Vishnevsky1,2,* and Nikolay A. Kolchanov1,2

1Institute of Cytology and Genetics, SB RAS Lavrentyev Avenue, 10, Novosibirsk, 630090, Russia 2Novosibirsk State University Pirogova Street, 2, Novosibirsk, 630090, Russia

*To whom correspondence should be addressed. Tel: +7 3832 333119; Fax: +7 3832 331278; Email: oleg{at}bionet.nsc.ru

Received February 14, 2005. Revised April 13, 2005. Accepted April 13, 2005.

Reliable recognition of the promoters in eukaryotic genomes remains an open issue. This is largely owing to the poor understanding of the features of the structural–functional organization of the eukaryotic promoters essential for their function and recognition. However, it was demonstrated that detection of ensembles of regulatory signals characteristic of specific promoter groups increases the accuracy of promoter recognition and prediction of specific expression features of the queried genes. The ARGO_Motifs package was developed for the detection of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of the eukaryotic genes. The ARGO_Viewer package was developed for the recognition of tissue-specific gene promoters based on the presence and distribution of oligonucleotide motifs obtained by the ARGO_Motifs program. Analysis and recognition of tissue-specific promoters in five gene samples demonstrated high quality of promoter recognition. The public version of the ARGO system is available at http://wwwmgs2.bionet.nsc.ru/argo/ and http://emj-pc.ics.uci.edu/argo/.


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