MersV1, Ncbi, Merge, bibRecord, 001388

GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.

Identifieur interne : 001388 ( Ncbi/Merge ); précédent : 001387; suivant : 001389

GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.

Auteurs : Lauris Kaplinski [Estonie] ; Maarja Lepamets [Estonie] ; Maido Remm [Estonie]

Source :

GigaScience [ 2047-217X ] ; 2015.

RBID : pubmed:26640690

Descripteurs français

KwdFr :
- Analyse de séquence d'ADN (), Animaux, Génome, Génomique (), Humains, Logiciel.
MESH :
- Analyse de séquence d'ADN, Animaux, Génome, Génomique, Humains, Logiciel.

English descriptors

KwdEn :
- Animals, Genome, Genomics (methods), Humans, Sequence Analysis, DNA (methods), Software.
MESH :
- methods : Genomics, Sequence Analysis, DNA.
- Animals, Genome, Humans, Software.

Abstract

K-mer-based methods of genome analysis have attracted great interest because they do not require genome assembly and can be performed directly on sequencing reads. Many analysis tasks require one to compare k-mer lists from different sequences to find words that are either unique to a specific sequence or common to many sequences. However, no stand-alone k-mer analysis tool currently allows one to perform these algebraic set operations.

DOI: 10.1186/s13742-015-0097-y
PubMed: 26640690

Links toward previous steps (curation, corpus...)

to stream PubMed, to step Corpus: 001354
to stream PubMed, to step Curation: 001354
to stream PubMed, to step Checkpoint: 001540

Links to Exploration step

pubmed:26640690

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.</title>
<author><name sortKey="Kaplinski, Lauris" sort="Kaplinski, Lauris" uniqKey="Kaplinski L" first="Lauris" last="Kaplinski">Lauris Kaplinski</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.</nlm:affiliation>
<country xml:lang="fr">Estonie</country>
<wicri:regionArea>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu</wicri:regionArea>
<wicri:noRegion>Tartu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Lepamets, Maarja" sort="Lepamets, Maarja" uniqKey="Lepamets M" first="Maarja" last="Lepamets">Maarja Lepamets</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia.</nlm:affiliation>
<country xml:lang="fr">Estonie</country>
<wicri:regionArea>Department of Bioinformatics, University of Tartu, Riia 23, Tartu</wicri:regionArea>
<wicri:noRegion>Tartu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Remm, Maido" sort="Remm, Maido" uniqKey="Remm M" first="Maido" last="Remm">Maido Remm</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.</nlm:affiliation>
<country xml:lang="fr">Estonie</country>
<wicri:regionArea>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu</wicri:regionArea>
<wicri:noRegion>Tartu</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2015">2015</date>
<idno type="RBID">pubmed:26640690</idno>
<idno type="pmid">26640690</idno>
<idno type="doi">10.1186/s13742-015-0097-y</idno>
<idno type="wicri:Area/PubMed/Corpus">001354</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001354</idno>
<idno type="wicri:Area/PubMed/Curation">001354</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001354</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001540</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001540</idno>
<idno type="wicri:Area/Ncbi/Merge">001388</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.</title>
<author><name sortKey="Kaplinski, Lauris" sort="Kaplinski, Lauris" uniqKey="Kaplinski L" first="Lauris" last="Kaplinski">Lauris Kaplinski</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.</nlm:affiliation>
<country xml:lang="fr">Estonie</country>
<wicri:regionArea>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu</wicri:regionArea>
<wicri:noRegion>Tartu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Lepamets, Maarja" sort="Lepamets, Maarja" uniqKey="Lepamets M" first="Maarja" last="Lepamets">Maarja Lepamets</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia.</nlm:affiliation>
<country xml:lang="fr">Estonie</country>
<wicri:regionArea>Department of Bioinformatics, University of Tartu, Riia 23, Tartu</wicri:regionArea>
<wicri:noRegion>Tartu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Remm, Maido" sort="Remm, Maido" uniqKey="Remm M" first="Maido" last="Remm">Maido Remm</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.</nlm:affiliation>
<country xml:lang="fr">Estonie</country>
<wicri:regionArea>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu</wicri:regionArea>
<wicri:noRegion>Tartu</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">GigaScience</title>
<idno type="ISSN">2047-217X</idno>
<imprint><date when="2015" type="published">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Genome</term>
<term>Genomics (methods)</term>
<term>Humans</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Software</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN ()</term>
<term>Animaux</term>
<term>Génome</term>
<term>Génomique ()</term>
<term>Humains</term>
<term>Logiciel</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Genome</term>
<term>Humans</term>
<term>Software</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Animaux</term>
<term>Génome</term>
<term>Génomique</term>
<term>Humains</term>
<term>Logiciel</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">K-mer-based methods of genome analysis have attracted great interest because they do not require genome assembly and can be performed directly on sequencing reads. Many analysis tasks require one to compare k-mer lists from different sequences to find words that are either unique to a specific sequence or common to many sequences. However, no stand-alone k-mer analysis tool currently allows one to perform these algebraic set operations.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26640690</PMID>
<DateCompleted><Year>2016</Year>
<Month>07</Month>
<Day>12</Day>
</DateCompleted>
<DateRevised><Year>2020</Year>
<Month>04</Month>
<Day>16</Day>
</DateRevised>
<Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2047-217X</ISSN>
<JournalIssue CitedMedium="Print"><Volume>4</Volume>
<PubDate><Year>2015</Year>
</PubDate>
</JournalIssue>
<Title>GigaScience</Title>
<ISOAbbreviation>Gigascience</ISOAbbreviation>
</Journal>
<ArticleTitle>GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.</ArticleTitle>
<Pagination><MedlinePgn>58</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1186/s13742-015-0097-y</ELocationID>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">K-mer-based methods of genome analysis have attracted great interest because they do not require genome assembly and can be performed directly on sequencing reads. Many analysis tasks require one to compare k-mer lists from different sequences to find words that are either unique to a specific sequence or common to many sequences. However, no stand-alone k-mer analysis tool currently allows one to perform these algebraic set operations.</AbstractText>
<AbstractText Label="FINDINGS" NlmCategory="RESULTS">We have developed the GenomeTester4 toolkit, which contains a novel tool GListCompare for performing union, intersection and complement (difference) set operations on k-mer lists. We provide examples of how these general operations can be combined to solve a variety of biological analysis tasks.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">GenomeTester4 can be used to simplify k-mer list manipulation for many biological analysis tasks.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kaplinski</LastName>
<ForeName>Lauris</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Lepamets</LastName>
<ForeName>Maarja</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Remm</LastName>
<ForeName>Maido</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.</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>
<ArticleDate DateType="Electronic"><Year>2015</Year>
<Month>12</Month>
<Day>03</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>Gigascience</MedlineTA>
<NlmUniqueID>101596872</NlmUniqueID>
<ISSNLinking>2047-217X</ISSNLinking>
</MedlineJournalInfo>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016678" MajorTopicYN="Y">Genome</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">K-mers</Keyword>
<Keyword MajorTopicYN="N">Next-generation sequencing</Keyword>
<Keyword MajorTopicYN="N">Sequence analysis</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year>
<Month>04</Month>
<Day>17</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2015</Year>
<Month>11</Month>
<Day>11</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2015</Year>
<Month>12</Month>
<Day>8</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2015</Year>
<Month>12</Month>
<Day>8</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2016</Year>
<Month>7</Month>
<Day>13</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>epublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">26640690</ArticleId>
<ArticleId IdType="doi">10.1186/s13742-015-0097-y</ArticleId>
<ArticleId IdType="pii">97</ArticleId>
<ArticleId IdType="pmc">PMC4669650</ArticleId>
</ArticleIdList>
<ReferenceList><Reference><Citation>Nucleic Acids Res. 2014 Apr;42(8):e67</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24523352</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>BMC Bioinformatics. 2012;13 Suppl 19:S10</Citation>
<ArticleIdList><ArticleId IdType="pubmed">23282463</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>F1000Res. 2015 Sep 25;4:900</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26535114</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nucleic Acids Res. 2014 Jan;42(Database issue):D553-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24316578</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>BMC Genomics. 2008 Oct 31;9:517</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18976482</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Bioinformatics. 2011 Mar 15;27(6):764-70</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21217122</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Genome Res. 2012 Mar;22(3):557-67</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22147368</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nature. 2011 Oct 12;479(7372):223-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21993625</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Bioinformatics. 2014 Jul 15;30(14):1950-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24618471</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Bioinformatics. 2015 May 15;31(10):1569-76</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25609798</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Genome Biol. 2014 Mar 03;15(3):R46</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24580807</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nat Biotechnol. 2014 May;32(5):462-4</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24752080</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Bioinformatics. 2013 Mar 1;29(5):652-3</Citation>
<ArticleIdList><ArticleId IdType="pubmed">23325618</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
<affiliations><list><country><li>Estonie</li>
</country>
</list>
<tree><country name="Estonie"><noRegion><name sortKey="Kaplinski, Lauris" sort="Kaplinski, Lauris" uniqKey="Kaplinski L" first="Lauris" last="Kaplinski">Lauris Kaplinski</name>
</noRegion>
<name sortKey="Lepamets, Maarja" sort="Lepamets, Maarja" uniqKey="Lepamets M" first="Maarja" last="Lepamets">Maarja Lepamets</name>
<name sortKey="Remm, Maido" sort="Remm, Maido" uniqKey="Remm M" first="Maido" last="Remm">Maido Remm</name>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Merge

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001388 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd -nk 001388 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    Ncbi
   |étape=   Merge
   |type=    RBID
   |clé=     pubmed:26640690
   |texte=   GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i   -Sk "pubmed:26640690" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd   \
       | NlmPubMed2Wicri -a MersV1

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021

	Serveur d'exploration MERS
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration MERS

GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.

GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

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