Yv. Kondrakhin et al., CONSTRUCTION OF A GENERALIZED CONSENSUS MATRIX FOR RECOGNITION OF VERTEBRATE PRE-MESSENGER-RNA 3'-TERMINAL PROCESSING SITES, Computer applications in the biosciences, 10(6), 1994, pp. 597-603
Using a set of sequences of 63 cleavage/polyadenylation sites of verte
brate pre-mRNA, a generalized consensus matrix was constructed. The el
ements 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 polyadenyla
tion site in a nucleotide sequence, a multiplicative measure was obtai
ned using the elements of the generalized consensus matrix as weight f
actors. For any omega-long fragment of a nucleotide sequence, the esti
mated value of the functional mu was compared with the threshold value
mu. Based on the results obtained, we determined whether ol not the
given fragment is a processing site.