kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies.
Identifieur interne : 000C53 ( PubMed/Corpus ); précédent : 000C52; suivant : 000C54kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies.
Auteurs : Jochen Kruppa ; Erhard Van Der Vries ; Wendy K. Jo ; Alexander Postel ; Paul Becher ; Albert Osterhaus ; Klaus JungSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2017.
English descriptors
- KwdEn :
- MESH :
- genetics : Bacteria, Viruses.
- methods : Sequence Analysis, DNA, Sequence Analysis, RNA.
- Computer Graphics, Principal Component Analysis, Software.
Abstract
Bioinformatics methods often incorporate the frequency distribution of nulecobases or k-mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package 'kmerPyramid' that allows to display each sequence, based on its nucleobase or k-mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid. Using the computer mouse, the user can turn the pyramid's axes, zoom in and out and identify individual points. Additionally, the package provides the k-mer frequency matrices of about 2000 bacteria and 5000 virus reference sequences calculated from the NCBI RefSeq genbank. The 'kmerPyramid' can particularly be used for visualization of intra- and inter species differences.
DOI: 10.1093/bioinformatics/btx385
PubMed: 28633391
Links to Exploration step
pubmed:28633391Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies.</title><author><name sortKey="Kruppa, Jochen" sort="Kruppa, Jochen" uniqKey="Kruppa J" first="Jochen" last="Kruppa">Jochen Kruppa</name><affiliation><nlm:affiliation>Institute for Animal Breeding and Genetics.</nlm:affiliation></affiliation></author><author><name sortKey="Van Der Vries, Erhard" sort="Van Der Vries, Erhard" uniqKey="Van Der Vries E" first="Erhard" last="Van Der Vries">Erhard Van Der Vries</name><affiliation><nlm:affiliation>Research Center for Emerging Infections and Zoonoses (RIZ).</nlm:affiliation></affiliation></author><author><name sortKey="Jo, Wendy K" sort="Jo, Wendy K" uniqKey="Jo W" first="Wendy K" last="Jo">Wendy K. Jo</name><affiliation><nlm:affiliation>Research Center for Emerging Infections and Zoonoses (RIZ).</nlm:affiliation></affiliation></author><author><name sortKey="Postel, Alexander" sort="Postel, Alexander" uniqKey="Postel A" first="Alexander" last="Postel">Alexander Postel</name><affiliation><nlm:affiliation>Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Becher, Paul" sort="Becher, Paul" uniqKey="Becher P" first="Paul" last="Becher">Paul Becher</name><affiliation><nlm:affiliation>Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Osterhaus, Albert" sort="Osterhaus, Albert" uniqKey="Osterhaus A" first="Albert" last="Osterhaus">Albert Osterhaus</name><affiliation><nlm:affiliation>Research Center for Emerging Infections and Zoonoses (RIZ).</nlm:affiliation></affiliation></author><author><name sortKey="Jung, Klaus" sort="Jung, Klaus" uniqKey="Jung K" first="Klaus" last="Jung">Klaus Jung</name><affiliation><nlm:affiliation>Institute for Animal Breeding and Genetics.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28633391</idno><idno type="pmid">28633391</idno><idno type="doi">10.1093/bioinformatics/btx385</idno><idno type="wicri:Area/PubMed/Corpus">000C53</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000C53</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies.</title><author><name sortKey="Kruppa, Jochen" sort="Kruppa, Jochen" uniqKey="Kruppa J" first="Jochen" last="Kruppa">Jochen Kruppa</name><affiliation><nlm:affiliation>Institute for Animal Breeding and Genetics.</nlm:affiliation></affiliation></author><author><name sortKey="Van Der Vries, Erhard" sort="Van Der Vries, Erhard" uniqKey="Van Der Vries E" first="Erhard" last="Van Der Vries">Erhard Van Der Vries</name><affiliation><nlm:affiliation>Research Center for Emerging Infections and Zoonoses (RIZ).</nlm:affiliation></affiliation></author><author><name sortKey="Jo, Wendy K" sort="Jo, Wendy K" uniqKey="Jo W" first="Wendy K" last="Jo">Wendy K. Jo</name><affiliation><nlm:affiliation>Research Center for Emerging Infections and Zoonoses (RIZ).</nlm:affiliation></affiliation></author><author><name sortKey="Postel, Alexander" sort="Postel, Alexander" uniqKey="Postel A" first="Alexander" last="Postel">Alexander Postel</name><affiliation><nlm:affiliation>Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Becher, Paul" sort="Becher, Paul" uniqKey="Becher P" first="Paul" last="Becher">Paul Becher</name><affiliation><nlm:affiliation>Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Osterhaus, Albert" sort="Osterhaus, Albert" uniqKey="Osterhaus A" first="Albert" last="Osterhaus">Albert Osterhaus</name><affiliation><nlm:affiliation>Research Center for Emerging Infections and Zoonoses (RIZ).</nlm:affiliation></affiliation></author><author><name sortKey="Jung, Klaus" sort="Jung, Klaus" uniqKey="Jung K" first="Klaus" last="Jung">Klaus Jung</name><affiliation><nlm:affiliation>Institute for Animal Breeding and Genetics.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacteria (genetics)</term><term>Computer Graphics</term><term>Principal Component Analysis</term><term>Sequence Analysis, DNA (methods)</term><term>Sequence Analysis, RNA (methods)</term><term>Software</term><term>Viruses (genetics)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Graphics</term><term>Principal Component Analysis</term><term>Software</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Bioinformatics methods often incorporate the frequency distribution of nulecobases or k-mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package 'kmerPyramid' that allows to display each sequence, based on its nucleobase or k-mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid. Using the computer mouse, the user can turn the pyramid's axes, zoom in and out and identify individual points. Additionally, the package provides the k-mer frequency matrices of about 2000 bacteria and 5000 virus reference sequences calculated from the NCBI RefSeq genbank. The 'kmerPyramid' can particularly be used for visualization of intra- and inter species differences.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">28633391</PMID><DateCompleted><Year>2018</Year><Month>07</Month><Day>20</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>33</Volume><Issue>19</Issue><PubDate><Year>2017</Year><Month>Oct</Month><Day>01</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies.</ArticleTitle><Pagination><MedlinePgn>3115-3116</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btx385</ELocationID><Abstract><AbstractText Label="Summary" NlmCategory="UNASSIGNED">Bioinformatics methods often incorporate the frequency distribution of nulecobases or k-mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package 'kmerPyramid' that allows to display each sequence, based on its nucleobase or k-mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid. Using the computer mouse, the user can turn the pyramid's axes, zoom in and out and identify individual points. Additionally, the package provides the k-mer frequency matrices of about 2000 bacteria and 5000 virus reference sequences calculated from the NCBI RefSeq genbank. The 'kmerPyramid' can particularly be used for visualization of intra- and inter species differences.</AbstractText><AbstractText Label="Availability and implementation" NlmCategory="UNASSIGNED">The R-package 'kmerPyramid' is available from the GitHub website at https://github.com/jkruppa/kmerPyramid.</AbstractText><AbstractText Label="Contact" NlmCategory="UNASSIGNED">klaus.jung@tiho-hannover.de.</AbstractText><AbstractText Label="Supplementary information" NlmCategory="UNASSIGNED">Supplementary data are available at Bioinformatics online.</AbstractText><CopyrightInformation>© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kruppa</LastName><ForeName>Jochen</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute for Animal Breeding and Genetics.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van der Vries</LastName><ForeName>Erhard</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Research Center for Emerging Infections and Zoonoses (RIZ).</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jo</LastName><ForeName>Wendy K</ForeName><Initials>WK</Initials><AffiliationInfo><Affiliation>Research Center for Emerging Infections and Zoonoses (RIZ).</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Postel</LastName><ForeName>Alexander</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Becher</LastName><ForeName>Paul</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Osterhaus</LastName><ForeName>Albert</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Research Center for Emerging Infections and Zoonoses (RIZ).</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jung</LastName><ForeName>Klaus</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Institute for Animal Breeding and Genetics.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</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="D001419" MajorTopicYN="N">Bacteria</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003196" MajorTopicYN="N">Computer Graphics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D025341" MajorTopicYN="N">Principal Component Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014780" MajorTopicYN="N">Viruses</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>02</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>06</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>6</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>7</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>6</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28633391</ArticleId><ArticleId IdType="pii">3868723</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btx385</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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