Kmer-db: instant evolutionary distance estimation.
Identifieur interne : 000843 ( PubMed/Corpus ); précédent : 000842; suivant : 000844Kmer-db: instant evolutionary distance estimation.
Auteurs : Sebastian Deorowicz ; Adam Gudys ; Maciej Dlugosz ; Marek Kokot ; Agnieszka DanekSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2019.
English descriptors
- KwdEn :
- MESH :
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
Links to Exploration step
pubmed:29986074Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Kmer-db: instant evolutionary distance estimation.</title>
<author><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name>
<affiliation><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Gudys, Adam" sort="Gudys, Adam" uniqKey="Gudys A" first="Adam" last="Gudys">Adam Gudys</name>
<affiliation><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Dlugosz, Maciej" sort="Dlugosz, Maciej" uniqKey="Dlugosz M" first="Maciej" last="Dlugosz">Maciej Dlugosz</name>
<affiliation><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Kokot, Marek" sort="Kokot, Marek" uniqKey="Kokot M" first="Marek" last="Kokot">Marek Kokot</name>
<affiliation><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Danek, Agnieszka" sort="Danek, Agnieszka" uniqKey="Danek A" first="Agnieszka" last="Danek">Agnieszka Danek</name>
<affiliation><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2019">2019</date>
<idno type="RBID">pubmed:29986074</idno>
<idno type="pmid">29986074</idno>
<idno type="doi">10.1093/bioinformatics/bty610</idno>
<idno type="wicri:Area/PubMed/Corpus">000843</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000843</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Kmer-db: instant evolutionary distance estimation.</title>
<author><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name>
<affiliation><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Gudys, Adam" sort="Gudys, Adam" uniqKey="Gudys A" first="Adam" last="Gudys">Adam Gudys</name>
<affiliation><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Dlugosz, Maciej" sort="Dlugosz, Maciej" uniqKey="Dlugosz M" first="Maciej" last="Dlugosz">Maciej Dlugosz</name>
<affiliation><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Kokot, Marek" sort="Kokot, Marek" uniqKey="Kokot M" first="Marek" last="Kokot">Marek Kokot</name>
<affiliation><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Danek, Agnieszka" sort="Danek, Agnieszka" uniqKey="Danek A" first="Agnieszka" last="Danek">Agnieszka Danek</name>
<affiliation><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
</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="MESH" xml:lang="en"><term>Algorithms</term>
<term>Biological Evolution</term>
<term>Computational Biology</term>
<term>Genome</term>
<term>Software</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>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000843 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 000843 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= PubMed |étape= Corpus |type= RBID |clé= pubmed:29986074 |texte= Kmer-db: instant evolutionary distance estimation. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:29986074" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
This area was generated with Dilib version V0.6.33. |