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Article: A recursive method for solving haplotype frequencies with application to genetics

TitleA recursive method for solving haplotype frequencies with application to genetics
Authors
KeywordsHaplotypes
Loci
Recursive methods
SNPs
Issue Date2006
PublisherImperial College Press. The Journal's web site is located at http://www.worldscinet.com/jbcb/jbcb.shtml
Citation
Journal Of Bioinformatics And Computational Biology, 2006, v. 4 n. 6, p. 1269-1285 How to Cite?
AbstractMultiple loci analysis has become popular with the advanced developments 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 for the n loci problem is of O(n2n) operations and the memory requirement is of O(2n) locations for the 2n-by-2n matrix A. Numerical examples are given to demonstrate the effectiveness of our efficient solver. Finally, we apply our proposed method to analyze the haplotype classes for a set of single nucleotides polymorphisms (SNPs) from Hapmap data. © Imperial College Press.
Persistent Identifierhttp://hdl.handle.net/10722/75423
ISSN
2023 Impact Factor: 0.9
2023 SCImago Journal Rankings: 0.270
References

 

DC FieldValueLanguage
dc.contributor.authorNg, MKen_HK
dc.contributor.authorFung, ESen_HK
dc.contributor.authorLee, YFen_HK
dc.contributor.authorChing, WKen_HK
dc.date.accessioned2010-09-06T07:10:58Z-
dc.date.available2010-09-06T07:10:58Z-
dc.date.issued2006en_HK
dc.identifier.citationJournal Of Bioinformatics And Computational Biology, 2006, v. 4 n. 6, p. 1269-1285en_HK
dc.identifier.issn0219-7200en_HK
dc.identifier.urihttp://hdl.handle.net/10722/75423-
dc.description.abstractMultiple loci analysis has become popular with the advanced developments 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 for the n loci problem is of O(n2n) operations and the memory requirement is of O(2n) locations for the 2n-by-2n matrix A. Numerical examples are given to demonstrate the effectiveness of our efficient solver. Finally, we apply our proposed method to analyze the haplotype classes for a set of single nucleotides polymorphisms (SNPs) from Hapmap data. © Imperial College Press.en_HK
dc.languageengen_HK
dc.publisherImperial College Press. The Journal's web site is located at http://www.worldscinet.com/jbcb/jbcb.shtmlen_HK
dc.relation.ispartofJournal of Bioinformatics and Computational Biologyen_HK
dc.subjectHaplotypes-
dc.subjectLoci-
dc.subjectRecursive methods-
dc.subjectSNPs-
dc.subject.meshAlgorithmsen_HK
dc.subject.meshChromosome Mapping - methodsen_HK
dc.subject.meshComputer Simulationen_HK
dc.subject.meshGene Frequencyen_HK
dc.subject.meshHaplotypes - geneticsen_HK
dc.subject.meshModels, Geneticen_HK
dc.subject.meshPolymorphism, Single Nucleotide - geneticsen_HK
dc.subject.meshQuantitative Trait Loci - geneticsen_HK
dc.titleA recursive method for solving haplotype frequencies with application to geneticsen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0219-7200&volume=4&spage=1269&epage=1286&date=2007&atitle=A+Recursive+Method+for+Solving+Haplotype+Frequencies+with+Application+to+Geneticsen_HK
dc.identifier.emailChing, WK:wching@hku.hken_HK
dc.identifier.authorityChing, WK=rp00679en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1142/S0219720006002454en_HK
dc.identifier.pmid17245814-
dc.identifier.scopuseid_2-s2.0-33846545718en_HK
dc.identifier.hkuros125754en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-33846545718&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume4en_HK
dc.identifier.issue6en_HK
dc.identifier.spage1269en_HK
dc.identifier.epage1285en_HK
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridNg, MK=34571761900en_HK
dc.identifier.scopusauthoridFung, ES=36886537700en_HK
dc.identifier.scopusauthoridLee, YF=14527155400en_HK
dc.identifier.scopusauthoridChing, WK=13310265500en_HK
dc.identifier.issnl0219-7200-

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