Patent ID: 8494784

Claim:
A method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto, the method comprising the steps of: generating one or more patterns by processing a collection of known mature microRNA sequences, wherein the one or more patterns comprise one or more intra- and inter-species patterns of conserved sequence segments, and wherein generating one or more patterns by processing a collection of known mature microRNA sequences is carried out by a component executing on a hardware processor; generating a reverse complement of each generated pattern, wherein generating a reverse complement of each generated pattern is carried out by a component executing on a hardware processor; assigning one or more attributes to the reverse complement of the one or more generated patterns, wherein assigning one or more attributes to the reverse complement of the one or more generated patterns is carried out by a component executing on a hardware processor; subselecting the one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion, wherein subselecting the one or more patterns is carried out by a component executing on a hardware processor, and wherein subselecting the one or more patterns comprises: statistically filtering the one or more patterns by estimating a log-probability of each pattern, wherein statistically filtering the one or more patterns by estimating a log-probability of each pattern comprises: using a Markov chain to estimate prior probabilities of multiple trinucleotide patterns spanning at most 23 positions and with, at most, 20 wild cards between the first and last nucleotide of each trinucleotide pattern; and using Bayes' theorem to calculate a posterior probability of each of the one or more patterns using the estimated prior probabilities of multiple trinucleotide patterns; using the one or more patterns that survive the statistical filtering to locate one or more instances of the one or more surviving patterns in a 3′UTR of the nucleotide sequence; and identifying one or more target areas in the nucleotide sequence supported by a minimum number of pattern instances; and using each subselected pattern to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto, wherein using each subselected pattern to analyze the nucleotide sequence comprises pairing each of the one or more target areas with each of one or more candidate microRNA sequences, identifying one or more target area-microRNA pairs whose interaction exceeds a predetermined threshold and disregarding any pair with a folding energy greater than a predetermined threshold, and wherein using each subselected pattern to analyze the nucleotide sequence is carried out by a component executing on a hardware processor.