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dc.contributor.authorKonagurthu, AS
dc.contributor.authorStuckey, PJ
dc.date.available2014-05-21T22:52:02Z
dc.date.issued2006-04-01
dc.identifierhttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000237966000005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=d4d813f4571fa7d6246bdc0dfeca3a1c
dc.identifier.citationKonagurthu, A. S. & Stuckey, P. J. (2006). Optimal sum-of-pairs multiple sequence alignment using incremental Carrillo and Lipman bounds. JOURNAL OF COMPUTATIONAL BIOLOGY, 13 (3), pp.668-685. https://doi.org/10.1089/cmb.2006.13.668.
dc.identifier.issn1066-5277
dc.identifier.urihttp://hdl.handle.net/11343/29304
dc.description.abstractAlignment of sequences is an important routine in various areas of science, notably molecular biology. Multiple sequence alignment is a computationally hard optimization problem which involves the consideration of different possible alignments in order to find an optimal one, given a measure of goodness of alignments. Dynamic programming algorithms are generally well suited for the search of optimal alignments, but are constrained by unwieldy space requirements for large numbers of sequences. Carrillo and Lipman devised a method that helps to reduce the search space for an optimal alignment under a sum-of-pairs measure using bounds on the scores of its pairwise projections. In this paper, we generalize Carrillo and Lipman bounds and demonstrate a novel approach for finding optimal sum-of-pairs multiple alignments that allows incremental pruning of the optimal alignment search space. This approach can result in a drastic pruning of the final search space polytope (where we search for the optimal alignment) when compared to Carrillo and Lipman's approach and hence allows many runs that are not feasible with the original method.
dc.languageEnglish
dc.publisherMARY ANN LIEBERT, INC
dc.subjectArtificial Intelligence and Image Processing
dc.titleOptimal sum-of-pairs multiple sequence alignment using incremental Carrillo and Lipman bounds
dc.typeJournal Article
dc.identifier.doi10.1089/cmb.2006.13.668
melbourne.peerreviewPeer Reviewed
melbourne.affiliationThe University of Melbourne
melbourne.affiliation.departmentComputer Science and Software Engineering
melbourne.source.titleJOURNAL OF COMPUTATIONAL BIOLOGY
melbourne.source.volume13
melbourne.source.issue3
melbourne.source.pages668-685
dc.description.pagestart668
melbourne.publicationid55938
melbourne.elementsid279860
melbourne.contributor.authorStuckey, Peter
melbourne.contributor.authorKONAGURTHU, ARUN SIDDHARTHA
dc.identifier.eissn1557-8666
melbourne.accessrightsThis item is currently not available from this repository


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