Kmer-db: instant evolutionary distance estimation.
Identifieur interne : 001E93 ( Ncbi/Merge ); précédent : 001E92; suivant : 001E94Kmer-db: instant evolutionary distance estimation.
Auteurs : Sebastian Deorowicz [Pologne] ; Adam Gudys [Pologne] ; Maciej Dlugosz [Pologne] ; Marek Kokot [Pologne] ; Agnieszka Danek [Pologne]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2019.
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Abstract
Kmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an efficient data structure and parallel implementation, our software estimates distances between 40 715 pathogens in <7 min (on a modern workstation), 26 times faster than Mash, its main competitor.
DOI: 10.1093/bioinformatics/bty610
PubMed: 29986074
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estimation.</title><author><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice</wicri:regionArea><wicri:noRegion>Gliwice</wicri:noRegion></affiliation></author><author><name sortKey="Gudys, Adam" sort="Gudys, Adam" uniqKey="Gudys A" first="Adam" last="Gudys">Adam Gudys</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation><country 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Kokot</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice</wicri:regionArea><wicri:noRegion>Gliwice</wicri:noRegion></affiliation></author><author><name sortKey="Danek, Agnieszka" sort="Danek, Agnieszka" uniqKey="Danek A" first="Agnieszka" last="Danek">Agnieszka Danek</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice</wicri:regionArea><wicri:noRegion>Gliwice</wicri:noRegion></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Biological Evolution</term><term>Computational Biology</term><term>Genome</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Biologie informatique</term><term>Génome</term><term>Logiciel</term><term>Évolution biologique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Biological Evolution</term><term>Computational Biology</term><term>Genome</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Biologie informatique</term><term>Génome</term><term>Logiciel</term><term>Évolution biologique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Kmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an efficient data structure and parallel implementation, our software estimates distances between 40 715 pathogens in <7 min (on a modern workstation), 26 times faster than Mash, its main competitor.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">29986074</PMID><DateCompleted><Year>2019</Year><Month>10</Month><Day>23</Day></DateCompleted><DateRevised><Year>2019</Year><Month>10</Month><Day>23</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>35</Volume><Issue>1</Issue><PubDate><Year>2019</Year><Month>01</Month><Day>01</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Kmer-db: instant evolutionary distance estimation.</ArticleTitle><Pagination><MedlinePgn>133-136</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/bty610</ELocationID><Abstract><AbstractText Label="Summary">Kmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an efficient data structure and parallel implementation, our software estimates distances between 40 715 pathogens in <7 min (on a modern workstation), 26 times faster than Mash, its main competitor.</AbstractText><AbstractText Label="Availability and implementation">https://github.com/refresh-bio/kmer-db and http://sun.aei.polsl.pl/REFRESH/kmer-db.</AbstractText><AbstractText Label="Supplementary information">Supplementary data are available at Bioinformatics online.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Deorowicz</LastName><ForeName>Sebastian</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gudys</LastName><ForeName>Adam</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dlugosz</LastName><ForeName>Maciej</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kokot</LastName><ForeName>Marek</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Danek</LastName><ForeName>Agnieszka</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="Y">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005075" MajorTopicYN="Y">Biological Evolution</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="Y">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016678" MajorTopicYN="N">Genome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>02</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>07</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>7</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>10</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>7</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29986074</ArticleId><ArticleId IdType="pii">5050791</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/bty610</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Pologne</li></country></list><tree><country name="Pologne"><noRegion><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name></noRegion><name sortKey="Danek, Agnieszka" sort="Danek, Agnieszka" uniqKey="Danek A" first="Agnieszka" last="Danek">Agnieszka Danek</name><name sortKey="Dlugosz, Maciej" sort="Dlugosz, Maciej" uniqKey="Dlugosz M" first="Maciej" last="Dlugosz">Maciej Dlugosz</name><name sortKey="Gudys, Adam" sort="Gudys, Adam" uniqKey="Gudys A" first="Adam" last="Gudys">Adam Gudys</name><name sortKey="Kokot, Marek" sort="Kokot, Marek" uniqKey="Kokot M" first="Marek" last="Kokot">Marek Kokot</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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