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.
Kondrakhin YuV
Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk.
Shamin
V V
VV
Kolchanov
N A
NA
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D008969:Molecular Sequence Data; D015394:Molecular Structure; D011061:Poly A / Q000378:metabolism; D012322:RNA Precursors / Q000737:chemistry* / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D013698:Templates, Genetic; D014158:Transcription, Genetic; D014714:Vertebrates / Q000235:genetics
D012322:RNA Precursors; D012333:RNA, Messenger; D011061:Poly A