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Conference Paper: Local structural alignment of RNA with affine gap model

TitleLocal structural alignment of RNA with affine gap model
Authors
Issue Date2011
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcproc
Citation
The 6th International Symposium on Bioinformatics Research and Applications (ISBRA'10), Storrs, CT., 23-26 May 2010. In BMC Proceedings, 2011, v. 5 suppl. 2, article no. S2 How to Cite?
AbstractBACKGROUND: 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.
Persistent Identifierhttp://hdl.handle.net/10722/140795
ISSN
2015 SCImago Journal Rankings: 0.445
PubMed Central ID

 

DC FieldValueLanguage
dc.contributor.authorWong, TKFen_US
dc.contributor.authorCheung, BWYen_US
dc.contributor.authorLam, TWen_US
dc.contributor.authorYiu, SMen_US
dc.date.accessioned2011-09-23T06:19:27Z-
dc.date.available2011-09-23T06:19:27Z-
dc.date.issued2011en_US
dc.identifier.citationThe 6th International Symposium on Bioinformatics Research and Applications (ISBRA'10), Storrs, CT., 23-26 May 2010. In BMC Proceedings, 2011, v. 5 suppl. 2, article no. S2en_US
dc.identifier.issn1753-6561-
dc.identifier.urihttp://hdl.handle.net/10722/140795-
dc.description.abstractBACKGROUND: 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.-
dc.languageengen_US
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcproc-
dc.relation.ispartofBMC Proceedingsen_US
dc.rightsBMC Proceedings. Copyright © BioMed Central Ltd.-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titleLocal structural alignment of RNA with affine gap modelen_US
dc.typeConference_Paperen_US
dc.identifier.emailWong, TKF: kfwong@cs.hku.hken_US
dc.identifier.emailLam, TW: hresltk@hkucc.hku.hken_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hk-
dc.identifier.authorityLam, TW=rp00135en_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/1753-6561-5-S2-S2-
dc.identifier.pmid21554760-
dc.identifier.pmcidPMC3090760-
dc.identifier.hkuros192234en_US
dc.identifier.hkuros177376-
dc.identifier.volume5en_US
dc.identifier.issuesuppl. 2, article no. S2en_US
dc.publisher.placeUnited Kingdom-
dc.customcontrol.immutablesml 151014-

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