GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.
Identifieur interne : 001354 ( PubMed/Corpus ); précédent : 001353; suivant : 001355GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.
Auteurs : Lauris Kaplinski ; Maarja Lepamets ; Maido RemmSource :
- GigaScience [ 2047-217X ] ; 2015.
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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
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<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><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.</nlm:affiliation></affiliation></author><author><name sortKey="Lepamets, Maarja" sort="Lepamets, Maarja" uniqKey="Lepamets M" first="Maarja" last="Lepamets">Maarja Lepamets</name><affiliation><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia.</nlm:affiliation></affiliation></author><author><name sortKey="Remm, Maido" sort="Remm, Maido" uniqKey="Remm M" first="Maido" last="Remm">Maido Remm</name><affiliation><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.</nlm:affiliation></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></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><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.</nlm:affiliation></affiliation></author><author><name sortKey="Lepamets, Maarja" sort="Lepamets, Maarja" uniqKey="Lepamets M" first="Maarja" last="Lepamets">Maarja Lepamets</name><affiliation><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia.</nlm:affiliation></affiliation></author><author><name sortKey="Remm, Maido" sort="Remm, Maido" uniqKey="Remm M" first="Maido" last="Remm">Maido Remm</name><affiliation><nlm:affiliation>Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.</nlm:affiliation></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="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></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 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