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

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 l 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 multiplicative measure was obtained using the elements of the generalized consensus matrix as weight factors. For any omega-long fragment of a nucleotide sequence, the estimated value of the functional mu was compared with the threshold value mu*. Based on the results obtained, we determined whether or not the given fragment is a processing site.