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Book Chapter: A recursive method for solving haplotype frequencies in multiple loci linkage analysis

TitleA recursive method for solving haplotype frequencies in multiple loci linkage analysis
Authors
Issue Date2006
PublisherWorld Scientific Publishing Co Pte Ltd. The Journal's web site is located at http://www.worldscibooks.com/series/abcb_series.shtml
Citation
Series On Advances In Bioinformatics And Computational Biology, 2006, v. 3, p. 129-138 How to Cite?
AbstractMultiple loci analysis has become popular with the advanced development in biological experiments. A lot of studies have been focused on the biological and the statistical properties of such multiple loci analysis. In this paper, we study one of the important computational problems: solving the probabilities of haplotype classes from a large linear system Ax = b derived from the recombination events in multiple loci analysis. Since the size of the recombination matrix A increases exponentially with respect to the number of loci, fast solvers are required to deal with a large number of loci in the analysis. By exploiting the nice structure of the matrix A, we develop an efficient recursive algorithm for solving such structured linear systems. In particular, the complexity of the proposed algorithm is of O(mlogm) operations and the memory requirement is of O(m) locations where m is the size of the matrix A. Numerical examples are given to demonstrate the effectiveness of our efficient solver.
Persistent Identifierhttp://hdl.handle.net/10722/123603
ISBN
ISSN
References

 

DC FieldValueLanguage
dc.contributor.authorNg, MKen_HK
dc.contributor.authorFung, ESen_HK
dc.contributor.authorChing, WKen_HK
dc.contributor.authorLee, YFen_HK
dc.date.accessioned2010-09-26T12:15:27Z-
dc.date.available2010-09-26T12:15:27Z-
dc.date.issued2006en_HK
dc.identifier.citationSeries On Advances In Bioinformatics And Computational Biology, 2006, v. 3, p. 129-138en_HK
dc.identifier.isbn978-186094623-3-
dc.identifier.issn1751-6404en_HK
dc.identifier.urihttp://hdl.handle.net/10722/123603-
dc.description.abstractMultiple loci analysis has become popular with the advanced development in biological experiments. A lot of studies have been focused on the biological and the statistical properties of such multiple loci analysis. In this paper, we study one of the important computational problems: solving the probabilities of haplotype classes from a large linear system Ax = b derived from the recombination events in multiple loci analysis. Since the size of the recombination matrix A increases exponentially with respect to the number of loci, fast solvers are required to deal with a large number of loci in the analysis. By exploiting the nice structure of the matrix A, we develop an efficient recursive algorithm for solving such structured linear systems. In particular, the complexity of the proposed algorithm is of O(mlogm) operations and the memory requirement is of O(m) locations where m is the size of the matrix A. Numerical examples are given to demonstrate the effectiveness of our efficient solver.en_HK
dc.languageengen_HK
dc.publisherWorld Scientific Publishing Co Pte Ltd. The Journal's web site is located at http://www.worldscibooks.com/series/abcb_series.shtmlen_HK
dc.relation.ispartofSeries on Advances in Bioinformatics and Computational Biologyen_HK
dc.titleA recursive method for solving haplotype frequencies in multiple loci linkage analysisen_HK
dc.typeBook_Chapteren_HK
dc.identifier.emailChing, WK:wching@hku.hken_HK
dc.identifier.authorityChing, WK=rp00679en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.scopuseid_2-s2.0-84863059479en_HK
dc.identifier.hkuros114590en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-84863059479&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume3en_HK
dc.identifier.spage129en_HK
dc.identifier.epage138en_HK
dc.publisher.placeSingaporeen_HK
dc.identifier.scopusauthoridNg, MK=34571761900en_HK
dc.identifier.scopusauthoridFung, ES=36886537700en_HK
dc.identifier.scopusauthoridChing, WK=13310265500en_HK
dc.identifier.scopusauthoridLee, YF=54984755100en_HK

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