MersV1, PubMed, Corpus, bibRecord, 001F20

SlideSort: all pairs similarity search for short reads.

Identifieur interne : 001F20 ( PubMed/Corpus ); précédent : 001F19; suivant : 001F21

SlideSort: all pairs similarity search for short reads.

Auteurs : Kana Shimizu ; Koji Tsuda

Source :

Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2011.

RBID : pubmed:21148542

English descriptors

KwdEn :
- Algorithms, Base Sequence, Computational Biology (methods), Sequence Analysis, DNA (methods), Software.
MESH :
- methods : Computational Biology, Sequence Analysis, DNA.
- Algorithms, Base Sequence, Software.

Abstract

Recent progress in DNA sequencing technologies calls for fast and accurate algorithms that can evaluate sequence similarity for a huge amount of short reads. Searching similar pairs from a string pool is a fundamental process of de novo genome assembly, genome-wide alignment and other important analyses.

DOI: 10.1093/bioinformatics/btq677
PubMed: 21148542

Links to Exploration step

pubmed:21148542

Le document en format XML

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<author><name sortKey="Shimizu, Kana" sort="Shimizu, Kana" uniqKey="Shimizu K" first="Kana" last="Shimizu">Kana Shimizu</name>
<affiliation><nlm:affiliation>Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Japan.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Tsuda, Koji" sort="Tsuda, Koji" uniqKey="Tsuda K" first="Koji" last="Tsuda">Koji Tsuda</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2011">2011</date>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">SlideSort: all pairs similarity search for short reads.</title>
<author><name sortKey="Shimizu, Kana" sort="Shimizu, Kana" uniqKey="Shimizu K" first="Kana" last="Shimizu">Kana Shimizu</name>
<affiliation><nlm:affiliation>Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Japan.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Tsuda, Koji" sort="Tsuda, Koji" uniqKey="Tsuda K" first="Koji" last="Tsuda">Koji Tsuda</name>
</author>
</analytic>
<series><title level="j">Bioinformatics (Oxford, England)</title>
<idno type="eISSN">1367-4811</idno>
<imprint><date when="2011" type="published">2011</date>
</imprint>
</series>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Base Sequence</term>
<term>Computational Biology (methods)</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Software</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Base Sequence</term>
<term>Software</term>
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<front><div type="abstract" xml:lang="en">Recent progress in DNA sequencing technologies calls for fast and accurate algorithms that can evaluate sequence similarity for a huge amount of short reads. Searching similar pairs from a string pool is a fundamental process of de novo genome assembly, genome-wide alignment and other important analyses.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">21148542</PMID>
<DateCompleted><Year>2011</Year>
<Month>04</Month>
<Day>19</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>12</Month>
<Day>01</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>27</Volume>
<Issue>4</Issue>
<PubDate><Year>2011</Year>
<Month>Feb</Month>
<Day>15</Day>
</PubDate>
</JournalIssue>
<Title>Bioinformatics (Oxford, England)</Title>
<ISOAbbreviation>Bioinformatics</ISOAbbreviation>
</Journal>
<ArticleTitle>SlideSort: all pairs similarity search for short reads.</ArticleTitle>
<Pagination><MedlinePgn>464-70</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btq677</ELocationID>
<Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Recent progress in DNA sequencing technologies calls for fast and accurate algorithms that can evaluate sequence similarity for a huge amount of short reads. Searching similar pairs from a string pool is a fundamental process of de novo genome assembly, genome-wide alignment and other important analyses.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">In this study, we designed and implemented an exact algorithm SlideSort that finds all similar pairs from a string pool in terms of edit distance. Using an efficient pattern growth algorithm, SlideSort discovers chains of common k-mers to narrow down the search. Compared to existing methods based on single k-mers, our method is more effective in reducing the number of edit distance calculations. In comparison to backtracking methods such as BWA, our method is much faster in finding remote matches, scaling easily to tens of millions of sequences. Our software has an additional function of single link clustering, which is useful in summarizing short reads for further processing.</AbstractText>
<AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">Executable binary files and C++ libraries are available at http://www.cbrc.jp/~shimizu/slidesort/ for Linux and Windows.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Shimizu</LastName>
<ForeName>Kana</ForeName>
<Initials>K</Initials>
<AffiliationInfo><Affiliation>Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Tsuda</LastName>
<ForeName>Koji</ForeName>
<Initials>K</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
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<ArticleDate DateType="Electronic"><Year>2010</Year>
<Month>12</Month>
<Day>09</Day>
</ArticleDate>
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<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Bioinformatics</MedlineTA>
<NlmUniqueID>9808944</NlmUniqueID>
<ISSNLinking>1367-4803</ISSNLinking>
</MedlineJournalInfo>
<CitationSubset>IM</CitationSubset>
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<MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName>
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<MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName>
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<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
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<MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName>
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SlideSort: all pairs similarity search for short reads.

SlideSort: all pairs similarity search for short reads.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki