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Article: An efficient motif discovery algorithm with unknown motif length and number of binding sites.

TitleAn efficient motif discovery algorithm with unknown motif length and number of binding sites.
Authors
Leung, HCChin, FY
Keywordsbinding sites
consensus pattern
DNA sequences
gene regulatory
motif discovering
transcription factor
Issue Date2006
PublisherInderscience Publishers. The Journal's web site is located at http://www.inderscience.com/ijdmb
Citation
International Journal Of Data Mining And Bioinformatics, 2006, v. 1 n. 2, p. 201-215 How to Cite?
DOI: http://dx.doi.org/10.1504/IJDMB.2006.010856
AbstractMost motif discovery algorithms from DNA sequences require the motif's length as input. Styczynski et al. introduced the Extended (l,d)-Motif Problem (EMP) where the motif's length is not an input parameter. Unfortunately, their algorithm takes an unacceptably long time to run, e.g. over 3 months to discover a length-14 motif. Since the best motif may not be the longest nor have the largest number of binding sites, in this paper we further eliminate another input parameter about the minimum number of binding sites in order to provide more realistic/robust results. We also develop an efficient algorithm to solve EMP and this redefined problem.
Persistent Identifierhttp://hdl.handle.net/10722/152388
ISSN
1748-5673
2023 Impact Factor: 0.2
2023 SCImago Journal Rankings: 0.173
ISI Accession Number ID
WOS:000247735400006

 

DC FieldValueLanguage
dc.contributor.authorLeung, HCen_US
dc.contributor.authorChin, FYen_US
dc.date.accessioned2012-06-26T06:37:51Z-
dc.date.available2012-06-26T06:37:51Z-
dc.date.issued2006en_US
dc.identifier.citationInternational Journal Of Data Mining And Bioinformatics, 2006, v. 1 n. 2, p. 201-215en_US
dc.identifier.issn1748-5673en_US
dc.identifier.urihttp://hdl.handle.net/10722/152388-
dc.description.abstractMost motif discovery algorithms from DNA sequences require the motif's length as input. Styczynski et al. introduced the Extended (l,d)-Motif Problem (EMP) where the motif's length is not an input parameter. Unfortunately, their algorithm takes an unacceptably long time to run, e.g. over 3 months to discover a length-14 motif. Since the best motif may not be the longest nor have the largest number of binding sites, in this paper we further eliminate another input parameter about the minimum number of binding sites in order to provide more realistic/robust results. We also develop an efficient algorithm to solve EMP and this redefined problem.en_US
dc.languageengen_US
dc.publisherInderscience Publishers. The Journal's web site is located at http://www.inderscience.com/ijdmben_US
dc.relation.ispartofInternational journal of data mining and bioinformaticsen_US
dc.subjectbinding sites-
dc.subjectconsensus pattern-
dc.subjectDNA sequences-
dc.subjectgene regulatory-
dc.subjectmotif discovering-
dc.subjecttranscription factor-
dc.subject.meshAlgorithmsen_US
dc.subject.meshAmino Acid Motifsen_US
dc.subject.meshBinding Sitesen_US
dc.subject.meshProteins - Chemistryen_US
dc.titleAn efficient motif discovery algorithm with unknown motif length and number of binding sites.en_US
dc.typeArticleen_US
dc.identifier.emailLeung, HC:cmleung2@cs.hku.hken_US
dc.identifier.emailChin, FY:chin@cs.hku.hken_US
dc.identifier.authorityLeung, HC=rp00144en_US
dc.identifier.authorityChin, FY=rp00105en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1504/IJDMB.2006.010856en_US
dc.identifier.pmid18399071-
dc.identifier.scopuseid_2-s2.0-43549118416en_US
dc.identifier.hkuros126290-
dc.identifier.volume1en_US
dc.identifier.issue2en_US
dc.identifier.spage201en_US
dc.identifier.epage215en_US
dc.identifier.isiWOS:000247735400006-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridLeung, HC=35233742700en_US
dc.identifier.scopusauthoridChin, FY=7005101915en_US
dc.identifier.issnl1748-5673-

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