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© Oxford University Press

SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites

A.E. Kel , M.P. Ponomarenko , E.A. Likhachev , Yu.L. Orlov , I.V. Ischenko , L. Milanesi 1 and N.A. Koichanov 2

Institute of Cytology and Genetics of the Russian Academy of Sciences, pr. Lavrentyeva 10, Novosibirsk, 630090, Russia
1Istituto di Tecnologie Biomediche Avanzate, Consiglio Nazionale Delle Ricerche Milano, Italy

2To whom reprint requests should be sent

We developed the computer system SITEVIDEO for analysis and recognition of the functional sites in DNA and RNA molecules. It reveals contextual features essential for site function and thus enable the user to design efficient methods for recognition of the functional sites. We mainly considered only quantitative characteristics reflecting the uneven distribution of oligonucleotides in the sequences of functional sites of interest. The approach suggested makes use of available information about the hierarchical organization of the functional sites, and ensures highly precise prediction of the sites. The present analysis is concerned with the human donor and acceptor splice sites. A method for recognizing these sites in the sequences with an accuracy of {bsim}90% was developed.

Received on February 24, 1992; accepted on May 31, 1993

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