A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria
Identifieur interne : 000A96 ( Main/Exploration ); précédent : 000A95; suivant : 000A97A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria
Auteurs : Erki Aun [Estonie] ; Age Brauer [Estonie] ; Veljo Kisand [Estonie] ; Tanel Tenson [Estonie] ; Maido Remm [Estonie]Source :
- PLoS Computational Biology [ 1553-734X ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- génétique : ADN bactérien, Bactéries, Génome bactérien, Marqueurs génétiques.
- métabolisme : Bactéries.
- physiologie : ADN bactérien, Génome bactérien.
- Algorithmes, Alignement de séquences, Analyse de séquence d'ADN, Génomique, Logiciel, Phénotype.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Bacterial, Genetic Markers.
- genetics : Bacteria, Genome, Bacterial.
- metabolism : Bacteria.
- methods : Genomics.
- chemical , physiology : DNA, Bacterial, Genome, Bacterial.
- Algorithms, Phenotype, Sequence Alignment, Sequence Analysis, DNA, Software.
Abstract
We have developed an easy-to-use and memory-efficient method called PhenotypeSeeker that (a) identifies phenotype-specific k-mers, (b) generates a
Url:
DOI: 10.1371/journal.pcbi.1006434
PubMed: 30346947
PubMed Central: 6211763
Affiliations:
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Le document en format XML
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Institute of Molecular and Cell Biology, University of Tartu, Tartu</wicri:regionArea><wicri:noRegion>Tartu</wicri:noRegion></affiliation></author><author><name sortKey="Brauer, Age" sort="Brauer, Age" uniqKey="Brauer A" first="Age" last="Brauer">Age Brauer</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia</addr-line></nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu</wicri:regionArea><wicri:noRegion>Tartu</wicri:noRegion></affiliation></author><author><name sortKey="Kisand, Veljo" sort="Kisand, Veljo" uniqKey="Kisand V" first="Veljo" last="Kisand">Veljo Kisand</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Institute of Technology, University of Tartu, Tartu, Estonia</addr-line></nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Technology, University of Tartu, Tartu</wicri:regionArea><wicri:noRegion>Tartu</wicri:noRegion></affiliation></author><author><name sortKey="Tenson, Tanel" sort="Tenson, Tanel" uniqKey="Tenson T" first="Tanel" last="Tenson">Tanel Tenson</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Institute of Technology, University of Tartu, Tartu, Estonia</addr-line></nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Technology, University of Tartu, 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:aff id="aff001"><addr-line>Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia</addr-line></nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu</wicri:regionArea><wicri:noRegion>Tartu</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS Computational Biology</title><idno type="ISSN">1553-734X</idno><idno type="eISSN">1553-7358</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Bacteria (genetics)</term><term>Bacteria (metabolism)</term><term>DNA, Bacterial (genetics)</term><term>DNA, Bacterial (physiology)</term><term>Genetic Markers (genetics)</term><term>Genome, Bacterial (genetics)</term><term>Genome, Bacterial (physiology)</term><term>Genomics (methods)</term><term>Phenotype</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien (génétique)</term><term>ADN bactérien (physiologie)</term><term>Algorithmes</term><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Bactéries (génétique)</term><term>Bactéries (métabolisme)</term><term>Génome bactérien (génétique)</term><term>Génome bactérien (physiologie)</term><term>Génomique ()</term><term>Logiciel</term><term>Marqueurs génétiques (génétique)</term><term>Phénotype</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Bacterial</term><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term><term>Genome, Bacterial</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term><term>Bactéries</term><term>Génome bactérien</term><term>Marqueurs génétiques</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>ADN bactérien</term><term>Génome bactérien</term></keywords><keywords scheme="MESH" type="chemical" qualifier="physiology" xml:lang="en"><term>DNA, Bacterial</term><term>Genome, Bacterial</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Phenotype</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Génomique</term><term>Logiciel</term><term>Phénotype</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>We have developed an easy-to-use and memory-efficient method called PhenotypeSeeker that (a) identifies phenotype-specific k-mers, (b) generates a <italic>k</italic>-mer-based statistical model for predicting a given phenotype and (c) predicts the phenotype from the sequencing data of a given bacterial isolate. The method was validated on 167 <italic>Klebsiella pneumoniae</italic> isolates (virulence), 200 <italic>Pseudomonas aeruginosa</italic> isolates (ciprofloxacin resistance) and 459 <italic>Clostridium difficile</italic> isolates (azithromycin resistance). The phenotype prediction models trained from these datasets obtained the F1-measure of 0.88 on the <italic>K</italic>. <italic>pneumoniae</italic> test set, 0.88 on the <italic>P</italic>. <italic>aeruginosa</italic> test set and 0.97 on the <italic>C</italic>. <italic>difficile</italic> test set. The F1-measures were the same for assembled sequences and raw sequencing data; however, building the model from assembled genomes is significantly faster. On these datasets, the model building on a mid-range Linux server takes approximately 3 to 5 hours per phenotype if assembled genomes are used and 10 hours per phenotype if raw sequencing data are used. The phenotype prediction from assembled genomes takes less than one second per isolate. Thus, PhenotypeSeeker should be well-suited for predicting phenotypes from large sequencing datasets. PhenotypeSeeker is implemented in Python programming language, is open-source software and is available at GitHub (<ext-link ext-link-type="uri" xlink:href="https://github.com/bioinfo-ut/PhenotypeSeeker/">https://github.com/bioinfo-ut/PhenotypeSeeker/</ext-link>).</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kisand, V" uniqKey="Kisand V">V Kisand</name></author><author><name sortKey="Lettieri, T" uniqKey="Lettieri T">T Lettieri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Crofts, Ts" uniqKey="Crofts T">TS Crofts</name></author><author><name sortKey="Gasparrini, Aj" uniqKey="Gasparrini A">AJ Gasparrini</name></author><author><name sortKey="Dantas, G" uniqKey="Dantas G">G Dantas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bakour, S" uniqKey="Bakour S">S Bakour</name></author><author><name sortKey="Sankar, Sa" uniqKey="Sankar S">SA 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Chang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, L C" uniqKey="Ma L">L-C Ma</name></author><author><name sortKey="Fang, C T" uniqKey="Fang C">C-T Fang</name></author><author><name sortKey="Lee, C Z" uniqKey="Lee C">C-Z Lee</name></author><author><name sortKey="Shun, C T" uniqKey="Shun C">C-T Shun</name></author><author><name sortKey="Wang, J T" uniqKey="Wang J">J-T Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lai, Yc" uniqKey="Lai Y">YC Lai</name></author><author><name sortKey="Lin, G T" uniqKey="Lin G">G-T Lin</name></author><author><name sortKey="Yang, S L" uniqKey="Yang S">S-L Yang</name></author><author><name sortKey="Chang, H Y" uniqKey="Chang H">H-Y Chang</name></author><author><name sortKey="Peng, H L" uniqKey="Peng H">H-L Peng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bankevich, A" uniqKey="Bankevich A">A Bankevich</name></author><author><name 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R">R Knight</name></author><author><name sortKey="Maxwell, P" uniqKey="Maxwell P">P Maxwell</name></author><author><name sortKey="Birmingham, A" uniqKey="Birmingham A">A Birmingham</name></author><author><name sortKey="Carnes, J" uniqKey="Carnes J">J Carnes</name></author><author><name sortKey="Caporaso, Jg" uniqKey="Caporaso J">JG Caporaso</name></author><author><name sortKey="Easton, Bc" uniqKey="Easton B">BC Easton</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Josh Pasek, A" uniqKey="Josh Pasek A">A Josh Pasek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pedregosa, F" uniqKey="Pedregosa F">F Pedregosa</name></author><author><name sortKey="Varoquaux, G" uniqKey="Varoquaux G">G Varoquaux</name></author><author><name sortKey="Gramfort, A" uniqKey="Gramfort A">A Gramfort</name></author><author><name sortKey="Michel, V" uniqKey="Michel V">V Michel</name></author><author><name sortKey="Thirion, B" uniqKey="Thirion B">B Thirion</name></author><author><name sortKey="Grisel, O" uniqKey="Grisel O">O Grisel</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Estonie</li></country></list><tree><country name="Estonie"><noRegion><name sortKey="Aun, Erki" sort="Aun, Erki" uniqKey="Aun E" first="Erki" last="Aun">Erki Aun</name></noRegion><name sortKey="Brauer, Age" sort="Brauer, Age" uniqKey="Brauer A" first="Age" last="Brauer">Age Brauer</name><name sortKey="Kisand, Veljo" sort="Kisand, Veljo" uniqKey="Kisand V" first="Veljo" last="Kisand">Veljo Kisand</name><name sortKey="Remm, Maido" sort="Remm, Maido" uniqKey="Remm M" first="Maido" last="Remm">Maido Remm</name><name sortKey="Tenson, Tanel" sort="Tenson, Tanel" uniqKey="Tenson T" first="Tanel" last="Tenson">Tanel Tenson</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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