File Download
  Links for fulltext
     (May Require Subscription)
Supplementary

Article: The mutated subsequence problem and locating conserved genes

TitleThe mutated subsequence problem and locating conserved genes
Authors
Issue Date2005
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2005, v. 21 n. 10, p. 2271-2278 How to Cite?
AbstractMotivation: For the purpose of locating conserved genes in a whole genome scale, this paper proposes a new structural optimization problem called the Mutated Subsequence Problem, which gives consideration to possible mutations between two species (in the form of reversals and transpositions) when comparing the genomes. Results: A practical algorithm called mutated subsequence algorithm (MSS) is devised to solve this optimization problem, and it has been evaluated using different pairs of human and mouse chromosomes, and different pairs of virus genomes of Baculoviridae. MSS is found to be effective and efficient; in particular, MSS can reveal >90% of the conserved genes of human and mouse that have been reported in the literature. When compared with existing softwares MUMmer and MaxMinCluster, MSS uncovers 14 and 7% more genes on average, respectively. Furthermore, this paper shows a hybrid approach to integrate MUMmer or MaxMinCluster with MSS, which has better performance and reliability. © The Author 2005. Published by Oxford University Press. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/43621
ISSN
2015 Impact Factor: 5.766
2015 SCImago Journal Rankings: 4.643
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorChan, HLen_HK
dc.contributor.authorLam, TWen_HK
dc.contributor.authorSung, WKen_HK
dc.contributor.authorWong, PWHen_HK
dc.contributor.authorYiu, SMen_HK
dc.contributor.authorFan, Xen_HK
dc.date.accessioned2007-03-23T04:50:39Z-
dc.date.available2007-03-23T04:50:39Z-
dc.date.issued2005en_HK
dc.identifier.citationBioinformatics, 2005, v. 21 n. 10, p. 2271-2278en_HK
dc.identifier.issn1367-4803en_HK
dc.identifier.urihttp://hdl.handle.net/10722/43621-
dc.description.abstractMotivation: For the purpose of locating conserved genes in a whole genome scale, this paper proposes a new structural optimization problem called the Mutated Subsequence Problem, which gives consideration to possible mutations between two species (in the form of reversals and transpositions) when comparing the genomes. Results: A practical algorithm called mutated subsequence algorithm (MSS) is devised to solve this optimization problem, and it has been evaluated using different pairs of human and mouse chromosomes, and different pairs of virus genomes of Baculoviridae. MSS is found to be effective and efficient; in particular, MSS can reveal >90% of the conserved genes of human and mouse that have been reported in the literature. When compared with existing softwares MUMmer and MaxMinCluster, MSS uncovers 14 and 7% more genes on average, respectively. Furthermore, this paper shows a hybrid approach to integrate MUMmer or MaxMinCluster with MSS, which has better performance and reliability. © The Author 2005. Published by Oxford University Press. All rights reserved.en_HK
dc.format.extent242332 bytes-
dc.format.extent26112 bytes-
dc.format.mimetypeapplication/pdf-
dc.format.mimetypeapplication/msword-
dc.languageengen_HK
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/en_HK
dc.relation.ispartofBioinformaticsen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshAlgorithmsen_HK
dc.subject.meshChromosome mapping - methodsen_HK
dc.subject.meshConserved sequence - geneticsen_HK
dc.subject.meshDna mutational analysis - methodsen_HK
dc.subject.meshEvolution, molecularen_HK
dc.titleThe mutated subsequence problem and locating conserved genesen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1471-2105&volume=21&issue=10&spage=2271&epage=2278&date=2005&atitle=The+mutated+subsequence+problem+and+locating+conserved+genesen_HK
dc.identifier.emailChan, HL:hlchan@cs.hku.hken_HK
dc.identifier.emailLam, TW:twlam@cs.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.authorityChan, HL=rp01310en_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1093/bioinformatics/bti371en_HK
dc.identifier.pmid15746277-
dc.identifier.scopuseid_2-s2.0-19544392024en_HK
dc.identifier.hkuros100156-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-19544392024&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume21en_HK
dc.identifier.issue10en_HK
dc.identifier.spage2271en_HK
dc.identifier.epage2278en_HK
dc.identifier.isiWOS:000229285600016-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridChan, HL=7403402384en_HK
dc.identifier.scopusauthoridLam, TW=7202523165en_HK
dc.identifier.scopusauthoridSung, WK=13310059700en_HK
dc.identifier.scopusauthoridWong, PWH=9734871500en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK
dc.identifier.scopusauthoridFan, X=23392609900en_HK
dc.identifier.citeulike205012-

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats