File Download

There are no files associated with this item.

  Links for fulltext
     (May Require Subscription)
Supplementary

Conference Paper: An experimental study of compressed indexing and local alignments of DNA

TitleAn experimental study of compressed indexing and local alignments of DNA
Authors
Issue Date2007
PublisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
Citation
Lecture Notes In Computer Science (Including Subseries Lecture Notes In Artificial Intelligence And Lecture Notes In Bioinformatics), 2007, v. 4616 LNCS, p. 241-254 How to Cite?
Abstract
Recent experimental studies on compressed indexes (BWT, CSA, FM-index) have confirmed their practicality for indexing long DNA sequences such as the human genome (about 3 billion characters) in the main memory [5,13,16]. However, these indexes are designed for exact pattern matching, which is too stringent for most biological applications. The demand is often on finding local alignments (pairs of similar sub-strings with gaps allowed). In this paper, we show how to build a software called BWT-SW that exploits a BWT index of a text T to speed up the dynamic programming for finding all local alignments with any pattern P. Experiments reveal that BWT-SW is very efficient (e.g., aligning a pattern of length 3,000 with the human genome takes less than a minute). We have also analyzed BWT-SW mathematically, using a simpler model (with gaps disallowed) and random strings. We find that the expected running time is O(|T| 0,628|P|). As far as we know, BWT-SW is the first practical tool that can find all local alignments. © Springer-Verlag Berlin Heidelberg 2007.
Persistent Identifierhttp://hdl.handle.net/10722/93144
ISSN
2013 SCImago Journal Rankings: 0.310
References

 

DC FieldValueLanguage
dc.contributor.authorLam, TWen_HK
dc.contributor.authorSung, WKen_HK
dc.contributor.authorTam, SLen_HK
dc.contributor.authorWong, CKen_HK
dc.contributor.authorYiu, SMen_HK
dc.date.accessioned2010-09-25T14:52:13Z-
dc.date.available2010-09-25T14:52:13Z-
dc.date.issued2007en_HK
dc.identifier.citationLecture Notes In Computer Science (Including Subseries Lecture Notes In Artificial Intelligence And Lecture Notes In Bioinformatics), 2007, v. 4616 LNCS, p. 241-254en_HK
dc.identifier.issn0302-9743en_HK
dc.identifier.urihttp://hdl.handle.net/10722/93144-
dc.description.abstractRecent experimental studies on compressed indexes (BWT, CSA, FM-index) have confirmed their practicality for indexing long DNA sequences such as the human genome (about 3 billion characters) in the main memory [5,13,16]. However, these indexes are designed for exact pattern matching, which is too stringent for most biological applications. The demand is often on finding local alignments (pairs of similar sub-strings with gaps allowed). In this paper, we show how to build a software called BWT-SW that exploits a BWT index of a text T to speed up the dynamic programming for finding all local alignments with any pattern P. Experiments reveal that BWT-SW is very efficient (e.g., aligning a pattern of length 3,000 with the human genome takes less than a minute). We have also analyzed BWT-SW mathematically, using a simpler model (with gaps disallowed) and random strings. We find that the expected running time is O(|T| 0,628|P|). As far as we know, BWT-SW is the first practical tool that can find all local alignments. © Springer-Verlag Berlin Heidelberg 2007.en_HK
dc.languageengen_HK
dc.publisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/en_HK
dc.relation.ispartofLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)en_HK
dc.titleAn experimental study of compressed indexing and local alignments of DNAen_HK
dc.typeConference_Paperen_HK
dc.identifier.emailLam, TW:twlam@cs.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.scopuseid_2-s2.0-38149082263en_HK
dc.identifier.hkuros146741en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-38149082263&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume4616 LNCSen_HK
dc.identifier.spage241en_HK
dc.identifier.epage254en_HK
dc.publisher.placeGermanyen_HK
dc.identifier.scopusauthoridLam, TW=7202523165en_HK
dc.identifier.scopusauthoridSung, WK=13310059700en_HK
dc.identifier.scopusauthoridTam, SL=14042926200en_HK
dc.identifier.scopusauthoridWong, CK=7404953816en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats