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Conference Paper: High throughput short read alignment via bi-directional BWT

TitleHigh throughput short read alignment via bi-directional BWT
Authors
KeywordsBWT
Indexing data structure
Short read alignment
Issue Date2009
PublisherIEEE.
Citation
The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009), Washington, DC., 1-4 November 2009. In Proceedings of BIBM, 2009, p. 31-36 How to Cite?
AbstractThe advancement of sequencing technologies has made it feasible for researchers to consider many highthroughput biological applications. A core step of these applications is to align an enormous amount of short reads to a reference genome. For example, to resequence a human genome, billions of reads of 35 bp are produced in 1-2 weeks, putting a lot of pressure of faster software for alignment. Based on existing indexing and pattern matching technologies, several short read alignment software have been developed recently. Yet this is still strong need to further improve the speed. In this paper, we show a new indexing data structure called bi-directional BWT, which allows us to build the fastest software for aligning short reads. When compared with existing software (Bowtie is the best), our software is at least 3 times faster for finding unique best alignments, and 25 times faster for finding all possible alignments. We believe that bi-directional BWT is an interesting data structure on its own and could be applied to other pattern matching problems. Availability: http://www.bio5.cs.hku.hk:8080/P2BWT, where two human genomes are indexed for alignment. © 2009 IEEE.
Persistent Identifierhttp://hdl.handle.net/10722/129577
ISBN
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorLam, TWen_HK
dc.contributor.authorLi, Ren_HK
dc.contributor.authorTam, Aen_HK
dc.contributor.authorWong, Sen_HK
dc.contributor.authorWu, Een_HK
dc.contributor.authorYiu, SMen_HK
dc.date.accessioned2010-12-23T08:39:26Z-
dc.date.available2010-12-23T08:39:26Z-
dc.date.issued2009en_HK
dc.identifier.citationThe IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009), Washington, DC., 1-4 November 2009. In Proceedings of BIBM, 2009, p. 31-36en_HK
dc.identifier.isbn978-0-7695-3885-3-
dc.identifier.urihttp://hdl.handle.net/10722/129577-
dc.description.abstractThe advancement of sequencing technologies has made it feasible for researchers to consider many highthroughput biological applications. A core step of these applications is to align an enormous amount of short reads to a reference genome. For example, to resequence a human genome, billions of reads of 35 bp are produced in 1-2 weeks, putting a lot of pressure of faster software for alignment. Based on existing indexing and pattern matching technologies, several short read alignment software have been developed recently. Yet this is still strong need to further improve the speed. In this paper, we show a new indexing data structure called bi-directional BWT, which allows us to build the fastest software for aligning short reads. When compared with existing software (Bowtie is the best), our software is at least 3 times faster for finding unique best alignments, and 25 times faster for finding all possible alignments. We believe that bi-directional BWT is an interesting data structure on its own and could be applied to other pattern matching problems. Availability: http://www.bio5.cs.hku.hk:8080/P2BWT, where two human genomes are indexed for alignment. © 2009 IEEE.en_HK
dc.languageengen_US
dc.publisherIEEE.-
dc.relation.ispartofProceedings of the IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009en_HK
dc.rightsIEEE International Conference on Bioinformatics and Biomedicine. Copyright © IEEE.-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rights©2009 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.-
dc.subjectBWTen_HK
dc.subjectIndexing data structureen_HK
dc.subjectShort read alignmenten_HK
dc.titleHigh throughput short read alignment via bi-directional BWTen_HK
dc.typeConference_Paperen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=978-0-7695-3885-3&volume=&spage=31&epage=36&date=2009&atitle=High+throughput+short+read+alignment+via+bi-directional+BWT-
dc.identifier.emailLam, TW:twlam@cs.hku.hken_HK
dc.identifier.emailWu, E:ewu1@hkucc.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityWu, E=rp00193en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1109/BIBM.2009.42en_HK
dc.identifier.scopuseid_2-s2.0-74549131724en_HK
dc.identifier.hkuros177020en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-74549131724&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.spage31en_HK
dc.identifier.epage36en_HK
dc.identifier.isiWOS:000275900200006-
dc.description.otherThe IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009), Washington, DC., 1-4 November 2009. In Proceedings of BIBM, 2009, p. 31-36-
dc.identifier.scopusauthoridLam, TW=7202523165en_HK
dc.identifier.scopusauthoridLi, R=34975581600en_HK
dc.identifier.scopusauthoridTam, A=35318914400en_HK
dc.identifier.scopusauthoridWong, S=35319323100en_HK
dc.identifier.scopusauthoridWu, E=7202128034en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK
dc.identifier.citeulike6497555-

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