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Article: Algorithms for challenging motif problems

TitleAlgorithms for challenging motif problems
Authors
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. 1, p. 43-58 How to Cite?
AbstractPevzner and Sze have introduced the Planted (l,d) -Motif Problem to find similar patterns (motifs) in sequences which represent the promoter regions of co-regulated genes, where l is the length of the motif and d is the maximum Hamming distance around the similar patterns. Many algorithms have been developed to solve this motif problem. However, these algorithms either have long running times or do not guarantee the motif can be found. In this paper, we introduce new algorithms to solve this motif problem. Our algorithms can find motifs in reasonable time for not only the challenging (9, 2), (11, 3), (15, 5)-motif problems but for even longer motifs, say (20, 7), (30, 11) and (40, 15), which have never been seriously attempted by other researchers because of the large time and space required. Besides, our algorithms can be extended to find more complicated motifs structure called cis-regulatory modules (CRM). © Imperial College Press.
Persistent Identifierhttp://hdl.handle.net/10722/89121
ISSN
2015 Impact Factor: 0.785
2015 SCImago Journal Rankings: 0.525
References

 

DC FieldValueLanguage
dc.contributor.authorLeung, HCMen_HK
dc.contributor.authorChin, FYLen_HK
dc.date.accessioned2010-09-06T09:52:39Z-
dc.date.available2010-09-06T09:52:39Z-
dc.date.issued2006en_HK
dc.identifier.citationJournal Of Bioinformatics And Computational Biology, 2006, v. 4 n. 1, p. 43-58en_HK
dc.identifier.issn0219-7200en_HK
dc.identifier.urihttp://hdl.handle.net/10722/89121-
dc.description.abstractPevzner and Sze have introduced the Planted (l,d) -Motif Problem to find similar patterns (motifs) in sequences which represent the promoter regions of co-regulated genes, where l is the length of the motif and d is the maximum Hamming distance around the similar patterns. Many algorithms have been developed to solve this motif problem. However, these algorithms either have long running times or do not guarantee the motif can be found. In this paper, we introduce new algorithms to solve this motif problem. Our algorithms can find motifs in reasonable time for not only the challenging (9, 2), (11, 3), (15, 5)-motif problems but for even longer motifs, say (20, 7), (30, 11) and (40, 15), which have never been seriously attempted by other researchers because of the large time and space required. Besides, our algorithms can be extended to find more complicated motifs structure called cis-regulatory modules (CRM). © 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.subject.meshAlgorithmsen_HK
dc.subject.meshBinding Sites - geneticsen_HK
dc.subject.meshComputational Biologyen_HK
dc.subject.meshDNA - genetics - metabolismen_HK
dc.subject.meshPromoter Regions, Geneticen_HK
dc.subject.meshTranscription Factors - metabolismen_HK
dc.titleAlgorithms for challenging motif problemsen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0219-7200&volume=4&issue=1&spage=43&epage=58&date=2006&atitle=Algorithms+for+Challenging+Motif+Problemsen_HK
dc.identifier.emailLeung, HCM:cmleung2@cs.hku.hken_HK
dc.identifier.emailChin, FYL:chin@cs.hku.hken_HK
dc.identifier.authorityLeung, HCM=rp00144en_HK
dc.identifier.authorityChin, FYL=rp00105en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1142/S0219720006001692en_HK
dc.identifier.pmid16568541-
dc.identifier.scopuseid_2-s2.0-33645308223en_HK
dc.identifier.hkuros117581en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-33645308223&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume4en_HK
dc.identifier.issue1en_HK
dc.identifier.spage43en_HK
dc.identifier.epage58en_HK
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridLeung, HCM=35233742700en_HK
dc.identifier.scopusauthoridChin, FYL=7005101915en_HK

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