kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies.
Identifieur interne : 000B10 ( Main/Exploration ); précédent : 000B09; suivant : 000B11kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies.
Auteurs : Jochen Kruppa ; Erhard Van Der Vries ; Wendy K. Jo ; Alexander Postel [Allemagne] ; Paul Becher [Allemagne] ; Albert Osterhaus ; Klaus JungSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
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
Affiliations:
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Jo</name><affiliation><nlm:affiliation>Research Center for Emerging Infections and Zoonoses (RIZ).</nlm:affiliation><wicri:noCountry code="no comma">Research Center for Emerging Infections and Zoonoses (RIZ).</wicri:noCountry></affiliation></author><author><name sortKey="Postel, Alexander" sort="Postel, Alexander" uniqKey="Postel A" first="Alexander" last="Postel">Alexander Postel</name><affiliation wicri:level="3"><nlm:affiliation>Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Hanovre</settlement></placeName></affiliation></author><author><name sortKey="Becher, Paul" sort="Becher, Paul" uniqKey="Becher P" first="Paul" last="Becher">Paul Becher</name><affiliation wicri:level="3"><nlm:affiliation>Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Hanovre</settlement></placeName></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><wicri:noCountry code="no comma">Research Center for Emerging Infections and Zoonoses (RIZ).</wicri:noCountry></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><wicri:noCountry code="no comma">Institute for Animal Breeding and Genetics.</wicri:noCountry></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="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN ()</term><term>Analyse de séquence d'ARN ()</term><term>Analyse en composantes principales</term><term>Bactéries (génétique)</term><term>Infographie</term><term>Logiciel</term><term>Virus (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bactéries</term><term>Virus</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><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Analyse de séquence d'ARN</term><term>Analyse en composantes principales</term><term>Infographie</term><term>Logiciel</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><affiliations><list><country><li>Allemagne</li></country><region><li>Basse-Saxe</li></region><settlement><li>Hanovre</li></settlement></list><tree><noCountry><name sortKey="Jo, Wendy K" sort="Jo, Wendy K" uniqKey="Jo W" first="Wendy K" last="Jo">Wendy K. Jo</name><name sortKey="Jung, Klaus" sort="Jung, Klaus" uniqKey="Jung K" first="Klaus" last="Jung">Klaus Jung</name><name sortKey="Kruppa, Jochen" sort="Kruppa, Jochen" uniqKey="Kruppa J" first="Jochen" last="Kruppa">Jochen Kruppa</name><name sortKey="Osterhaus, Albert" sort="Osterhaus, Albert" uniqKey="Osterhaus A" first="Albert" last="Osterhaus">Albert Osterhaus</name><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></noCountry><country name="Allemagne"><region name="Basse-Saxe"><name sortKey="Postel, Alexander" sort="Postel, Alexander" uniqKey="Postel A" first="Alexander" last="Postel">Alexander Postel</name></region><name sortKey="Becher, Paul" sort="Becher, Paul" uniqKey="Becher P" first="Paul" last="Becher">Paul Becher</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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