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Conference Paper: An efficient algorithm for the extended (l,d)-motif problem with unknown number of binding sites

TitleAn efficient algorithm for the extended (l,d)-motif problem with unknown number of binding sites
Authors
Issue Date2005
PublisherIEEE, Computer Society.
Citation
Proceedings - Bibe 2005: 5Th Ieee Symposium On Bioinformatics And Bioengineering, 2005, v. 2005, p. 11-18 How to Cite?
AbstractFinding common patterns, or motifs, from a set of DNA sequences is an important problem in molecular biology. Most motif-discovering algorithms/software require the length of the motif as input. Motivated by the fact that the motif's length is usually unknown in practice, Styczynsfd et al. introduced the Extended (l,d)-Motif Problem (EMP), where the motif's length is not an input parameter. Unfortunately, the algorithm given by Styczynski et al. to solve EMP can take an unacceptably long time to run, e.g. over 3 months to discover a length-14 motif. This paper makes two main contributions. First, we eliminate another input parameter from EMP: the minimum number of binding sites in the DNA sequences. Fewer input parameters not only reduces the burden of the user, but also may give more realistic/robust results since restrictions on length or on the number of binding sites make little sense when the best motif may not be the longest nor have the largest number of binding sites. Second, we develop an efficient algorithm to solve our redefined problem. The algorithm is also a fast solution for EMP (without any sacrifice to accuracy) making EMP practical. © 2005 IEEE.
Persistent Identifierhttp://hdl.handle.net/10722/45554
References

 

DC FieldValueLanguage
dc.contributor.authorLeung, HCMen_HK
dc.contributor.authorChin, FYLen_HK
dc.date.accessioned2007-10-30T06:29:03Z-
dc.date.available2007-10-30T06:29:03Z-
dc.date.issued2005en_HK
dc.identifier.citationProceedings - Bibe 2005: 5Th Ieee Symposium On Bioinformatics And Bioengineering, 2005, v. 2005, p. 11-18en_HK
dc.identifier.urihttp://hdl.handle.net/10722/45554-
dc.description.abstractFinding common patterns, or motifs, from a set of DNA sequences is an important problem in molecular biology. Most motif-discovering algorithms/software require the length of the motif as input. Motivated by the fact that the motif's length is usually unknown in practice, Styczynsfd et al. introduced the Extended (l,d)-Motif Problem (EMP), where the motif's length is not an input parameter. Unfortunately, the algorithm given by Styczynski et al. to solve EMP can take an unacceptably long time to run, e.g. over 3 months to discover a length-14 motif. This paper makes two main contributions. First, we eliminate another input parameter from EMP: the minimum number of binding sites in the DNA sequences. Fewer input parameters not only reduces the burden of the user, but also may give more realistic/robust results since restrictions on length or on the number of binding sites make little sense when the best motif may not be the longest nor have the largest number of binding sites. Second, we develop an efficient algorithm to solve our redefined problem. The algorithm is also a fast solution for EMP (without any sacrifice to accuracy) making EMP practical. © 2005 IEEE.en_HK
dc.format.extent172013 bytes-
dc.format.extent5052 bytes-
dc.format.mimetypeapplication/pdf-
dc.format.mimetypetext/plain-
dc.languageengen_HK
dc.publisherIEEE, Computer Society.en_HK
dc.relation.ispartofProceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineeringen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rights©2005 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.titleAn efficient algorithm for the extended (l,d)-motif problem with unknown number of binding sitesen_HK
dc.typeConference_Paperen_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.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1109/BIBE.2005.12en_HK
dc.identifier.scopuseid_2-s2.0-33751167615en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-33751167615&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume2005en_HK
dc.identifier.spage11en_HK
dc.identifier.epage18en_HK
dc.identifier.scopusauthoridLeung, HCM=35233742700en_HK
dc.identifier.scopusauthoridChin, FYL=7005101915en_HK
dc.identifier.citeulike4313183-

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