Patent ID: 8116987

Claim:
A computer-implemented method of identifying microRNA precursor candidates in non-coding and coding regions of a genome, comprising: receiving at least a first and a second genome from two different species, each containing a plurality of sequences including highly repetitive DNA; masking a first set of highly repetitive DNA sequences in the first genome, wherein the first set includes SINE and LINE interspersed repeat sequences, but does not include at least 75% of other interspersed repeat sequences; masking a second set of highly repetitive DNA sequences in the second genome, wherein the second set includes SINE and LINE interspersed repeat sequences, but does not include at least 75% of the other interspersed repeat sequences; comparing the masked first genome to the masked second genome to determine pairs of sequences that are homologous between the two genomes; creating a list of microRNA precursor candidates from the homologous pairs; and analyzing, with a computer, the list of candidates to: eliminate sequences having less than 60 nucleotides; and identify sequences that have a stem-loop secondary structure with a 5′ strand stem having from 20 to 45 nucleotides and with a 3′ strand stem having from 20 to 45 nucleotides; and remove, from the list, sequences not having said stem-loop secondary structure, thereby identifying microRNA precursor candidates.