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Article: Detection of generic spaced motifs using submotif pattern mining

TitleDetection of generic spaced motifs using submotif pattern mining
Authors
Issue Date2007
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2007, v. 23 n. 12, p. 1476-1485 How to Cite?
Abstract
Motivation: Identification of motifs is one of the critical stages in studying the regulatory interactions of genes. Motifs can have complicated patterns. In particular, spaced motifs, an important class of motifs, consist of several short segments separated by spacers of different lengths. Locating spaced motifs is not trivial. Existing motif-finding algorithms are either designed for monad motifs (short contiguous patterns with some mismatches) or have assumptions on the spacer lengths or can only handle at most two segments. An effective motif finder for generic spaced motifs is highly desirable. Results: This article proposes a novel approach for identifying spaced motifs with any number of spacers of different lengths. We introduce the notion of submotifs to capture the segments in the spaced motif and formulate the motif-finding problem as a frequent submotif mining problem. We provide an algorithm called SPACE to solve the problem. Based on experiments on real biological datasets, synthetic datasets and the motif assessment benchmarks by Tompa et al., we show that our algorithm performs better than existing tools for spaced motifs with improvements in both sensitivity and specificity and for monads, SPACE performs as good as other tools. © The Author 2007. Published by Oxford University Press. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/88970
ISSN
2013 Impact Factor: 4.621
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWijaya, Een_HK
dc.contributor.authorRajaraman, Ken_HK
dc.contributor.authorYiu, SMen_HK
dc.contributor.authorSung, WKen_HK
dc.date.accessioned2010-09-06T09:50:45Z-
dc.date.available2010-09-06T09:50:45Z-
dc.date.issued2007en_HK
dc.identifier.citationBioinformatics, 2007, v. 23 n. 12, p. 1476-1485en_HK
dc.identifier.issn1367-4803en_HK
dc.identifier.urihttp://hdl.handle.net/10722/88970-
dc.description.abstractMotivation: Identification of motifs is one of the critical stages in studying the regulatory interactions of genes. Motifs can have complicated patterns. In particular, spaced motifs, an important class of motifs, consist of several short segments separated by spacers of different lengths. Locating spaced motifs is not trivial. Existing motif-finding algorithms are either designed for monad motifs (short contiguous patterns with some mismatches) or have assumptions on the spacer lengths or can only handle at most two segments. An effective motif finder for generic spaced motifs is highly desirable. Results: This article proposes a novel approach for identifying spaced motifs with any number of spacers of different lengths. We introduce the notion of submotifs to capture the segments in the spaced motif and formulate the motif-finding problem as a frequent submotif mining problem. We provide an algorithm called SPACE to solve the problem. Based on experiments on real biological datasets, synthetic datasets and the motif assessment benchmarks by Tompa et al., we show that our algorithm performs better than existing tools for spaced motifs with improvements in both sensitivity and specificity and for monads, SPACE performs as good as other tools. © The Author 2007. Published by Oxford University Press. All rights reserved.en_HK
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.subject.meshAmino Acid Motifs-
dc.subject.meshComputational Biology - methods-
dc.subject.meshPattern Recognition, Automated-
dc.subject.meshProtein Structure, Tertiary-
dc.subject.meshTranscription Factors/genetics-
dc.titleDetection of generic spaced motifs using submotif pattern miningen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1367-4803&volume=23&issue=12&spage=1476&epage=1485&date=2007&atitle=Detection+of+generic+spaced+motifs+using+submotif+pattern+miningen_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1093/bioinformatics/btm118en_HK
dc.identifier.pmid17483509en_HK
dc.identifier.scopuseid_2-s2.0-34547840183en_HK
dc.identifier.hkuros161322en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-34547840183&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume23en_HK
dc.identifier.issue12en_HK
dc.identifier.spage1476en_HK
dc.identifier.epage1485en_HK
dc.identifier.isiWOS:000248271700006-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridWijaya, E=26326005500en_HK
dc.identifier.scopusauthoridRajaraman, K=7003716909en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK
dc.identifier.scopusauthoridSung, WK=13310059700en_HK
dc.identifier.citeulike1365971-

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