Patent ID: 8014956

Claim:
A computer system for identifying a microRNA precursor, comprising: one or more processors configured to execute program instructions; and a computer-readable medium containing executable instructions that, when executed by the one or more processors, cause the computer system to perform a method for identifying a microRNA precursor, the method comprising: (a) providing a subject DNA sequence; (b) searching, by a heuristic algorithm, in the subject DNA sequence of step (a) for a DNA region that has a strong tendency to form a stem loop; (c) retaining a DNA region of step (b) that does not reside in a low complexity region of the subject DNA sequence of step (a); (d) assessing the ability of the retained DNA region of step (c) to fold into a secondary structure, and selecting a DNA region whose corresponding RNA sequence has a low energy of folding and forms a stem loop; (e) comparing the energy of folding of two selected DNA regions of step (d) that overlap with each other substantially such that both overlap ratios exceed a predetermined value, and choosing the one with the lowest energy of folding; (f) assessing the stability of a chosen DNA regions of step (e) by performing randomized shuffle of the chosen DNA region a number of times, while keeping a characteristic property of the chosen DNA region unchanged, and calculating a score as a measure of the stability of the secondary structure formed by the chosen DNA region; and (g) identifying, from one or more chosen DNA regions, a target section that has a stability score higher than a pre-determined value; whereby the target section is determined to be a microRNA precursor.