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© Oxford University Press

Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3'-terminal processing sites

Yu. V. Kondrakhin , V. V. Shamin 1 and N.A. Kolchanov

Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences Novosibirsk, 630090, Russia

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Using a set of sequences of 63 cleavage/polyadenylation sites of vertebrate pre-mRNA, a generalized consensus matrix was constructed. The elements of the matrix were the absolute frequencies of oligonucleotides of length I at the ith position of sites. The cleavage point of each site was assigned the same position number. To recognize a polyadenylation site in a nucleotide sequence, a multi plicative measure was obtained using the elements of the generalized consensus matrix as weight factors. For any w-long fragment of a nucleo tide sequence, the estimated value of the functional i was compared with the threshold value ,µ*. Based on the results obtained, we determined whether or not the given fragment is a processing site.


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