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Local structural alignment of RNA with affine gap model.

ABSTRACT: BACKGROUND:Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. RESULTS:In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. CONCLUSIONS:Based on an experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.

SUBMITTER: King-Fung Wong T

PROVIDER: S-EPMC3090760 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature

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Local structural alignment of RNA with affine gap model.

King-Fung Wong Thomas T Wing-Yan Cheung Brenda B Lam Tak-Wah TW Yiu Siu-Ming SM

BMC proceedings 20110528

<h4>Background</h4>Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps.<h4>Results</h4>In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown se ...[more]

PMID: 21554760

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