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Article: DNA motif representation with nucleotide dependency

TitleDNA motif representation with nucleotide dependency
Authors
KeywordsComputing methodologies
Design methodology
Pattern analysis
Pattern recognition
Issue Date2008
PublisherIEEE.
Citation
Ieee/Acm Transactions On Computational Biology And Bioinformatics, 2008, v. 5 n. 1, p. 110-119 How to Cite?
AbstractThe problem of discovering novel motifs of binding sites is important to the understanding of gene regulatory networks. Motifs are generally represented by matrices (position weight matrix (PWM) or position specific scoring matrix (PSSM)) or strings. However, these representations cannot model biological binding sites well because they fail to capture nucleotide interdependence. It has been pointed out by many researchers that the nucleotides of the DNA binding site cannot be treated independently, for example, the binding sites of zinc finger in proteins. In this paper, a new representation called Scored Position Specific Pattern (SPSP), which is a generalization of the matrix and string representations, is introduced, which takes into consideration the dependent occurrences of neighboring nucleotides. Even though the problem of discovering the optimal motif in SPSP representation is proved to be NP-hard, we introduce a heuristic algorithm called SPSP Finder, which can effectively find optimal motifs in most simulated cases and some real cases for which existing popular motif-finding software, such as Weeder, MEME, and AlignACE, fail. © 2008 IEEE.
Persistent Identifierhttp://hdl.handle.net/10722/57248
ISSN
2015 Impact Factor: 1.609
2015 SCImago Journal Rankings: 0.706
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorChin, Fen_HK
dc.contributor.authorLeung, HCMen_HK
dc.date.accessioned2010-04-12T01:30:48Z-
dc.date.available2010-04-12T01:30:48Z-
dc.date.issued2008en_HK
dc.identifier.citationIeee/Acm Transactions On Computational Biology And Bioinformatics, 2008, v. 5 n. 1, p. 110-119en_HK
dc.identifier.issn1545-5963en_HK
dc.identifier.urihttp://hdl.handle.net/10722/57248-
dc.description.abstractThe problem of discovering novel motifs of binding sites is important to the understanding of gene regulatory networks. Motifs are generally represented by matrices (position weight matrix (PWM) or position specific scoring matrix (PSSM)) or strings. However, these representations cannot model biological binding sites well because they fail to capture nucleotide interdependence. It has been pointed out by many researchers that the nucleotides of the DNA binding site cannot be treated independently, for example, the binding sites of zinc finger in proteins. In this paper, a new representation called Scored Position Specific Pattern (SPSP), which is a generalization of the matrix and string representations, is introduced, which takes into consideration the dependent occurrences of neighboring nucleotides. Even though the problem of discovering the optimal motif in SPSP representation is proved to be NP-hard, we introduce a heuristic algorithm called SPSP Finder, which can effectively find optimal motifs in most simulated cases and some real cases for which existing popular motif-finding software, such as Weeder, MEME, and AlignACE, fail. © 2008 IEEE.en_HK
dc.languageengen_HK
dc.publisherIEEE.en_HK
dc.relation.ispartofIEEE/ACM Transactions on Computational Biology and Bioinformaticsen_HK
dc.rights©2008 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.en_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subjectComputing methodologiesen_HK
dc.subjectDesign methodologyen_HK
dc.subjectPattern analysisen_HK
dc.subjectPattern recognitionen_HK
dc.subject.meshConserved Sequence - geneticsen_HK
dc.subject.meshPattern Recognition, Automated - methodsen_HK
dc.subject.meshRegulatory Sequences, Nucleic Acid - geneticsen_HK
dc.subject.meshSequence Analysis, DNA - methodsen_HK
dc.subject.meshBinding Sites - geneticsen_HK
dc.titleDNA motif representation with nucleotide dependencyen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1545-5963&volume=5&issue=1&spage=110&epage=119&date=2008&atitle=DNA+motif+representation+with+nucleotide+dependencyen_HK
dc.identifier.emailChin, F:chin@cs.hku.hken_HK
dc.identifier.emailLeung, HCM:cmleung2@cs.hku.hken_HK
dc.identifier.authorityChin, F=rp00105en_HK
dc.identifier.authorityLeung, HCM=rp00144en_HK
dc.description.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1109/TCBB.2007.70220en_HK
dc.identifier.pmid18245880-
dc.identifier.scopuseid_2-s2.0-38949129061en_HK
dc.identifier.hkuros141231-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-38949129061&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume5en_HK
dc.identifier.issue1en_HK
dc.identifier.spage110en_HK
dc.identifier.epage119en_HK
dc.identifier.isiWOS:000253417100010-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridChin, F=7005101915en_HK
dc.identifier.scopusauthoridLeung, HCM=35233742700en_HK
dc.identifier.citeulike2334707-

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