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US 8,014,956 B2Granted
MicroRNA precursors
AssigneeIndustrial Technology Research Institute
InventorsYu-Ching Chang, Yu-Yu Lin, Shiu-Chieh Lan, Cheng-Tao Wu, Chung-Cheng Liu
Life of this patent
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Abstract
Disclosed are methods of identifying microRNA motifs or microRNA precursors for a target gene or a set of target genes. Also disclosed are related computer-readable media.
Claims17
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.
9 more elements
A computer program product, comprising a tangible computer readable medium comprising executable instructions for effecting the following steps:
- (a) receiving a subject DNA sequence;
- (b) searching, by a heuristic algorithm, in the subject DNA sequence 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;
- (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;
- (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;
- and
- outputting the sequence of the microRNA precursor.
7 more elements
Dependencies are inferred from the claim text.