Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences
Identifieur interne : 000889 ( Main/Exploration ); précédent : 000888; suivant : 000890Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences
Auteurs : Amber L. Hartman [États-Unis] ; Sean Riddle [États-Unis] ; Timothy Mcphillips [États-Unis] ; Bertram Lud Scher [États-Unis] ; Jonathan A. Eisen [États-Unis]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2010.
Abstract
For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.
We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform.
By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.
Url:
DOI: 10.1186/1471-2105-11-317
PubMed: 20540779
PubMed Central: 2898799
Affiliations:
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Hartman</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Medical Microbiology and Immunology and the Department of Evolution and Ecology, Genome Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medical Microbiology and Immunology and the Department of Evolution and Ecology, Genome Center, University of California Davis, One Shields Avenue, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Department of Biology, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218</wicri:regionArea><wicri:noRegion>21218</wicri:noRegion></affiliation></author><author><name sortKey="Riddle, Sean" sort="Riddle, Sean" uniqKey="Riddle S" first="Sean" last="Riddle">Sean Riddle</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Computer Science, Genome Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Genome Center, University of California Davis, One Shields Avenue, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation></author><author><name sortKey="Mcphillips, Timothy" sort="Mcphillips, Timothy" uniqKey="Mcphillips T" first="Timothy" last="Mcphillips">Timothy Mcphillips</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Computer Science, Genome Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Genome Center, University of California Davis, One Shields Avenue, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation></author><author><name sortKey="Lud Scher, Bertram" sort="Lud Scher, Bertram" uniqKey="Lud Scher B" first="Bertram" last="Lud Scher">Bertram Lud Scher</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Computer Science, Genome Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Genome Center, University of California Davis, One Shields Avenue, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation></author><author><name sortKey="Eisen, Jonathan A" sort="Eisen, Jonathan A" uniqKey="Eisen J" first="Jonathan A" last="Eisen">Jonathan A. Eisen</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Medical Microbiology and Immunology and the Department of Evolution and Ecology, Genome Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medical Microbiology and Immunology and the Department of Evolution and Ecology, Genome Center, University of California Davis, One Shields Avenue, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.</p></sec><sec><title>Results</title><p>We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform.</p></sec><sec><title>Conclusions</title><p>By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Pace, Nr" uniqKey="Pace N">NR Pace</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carney, Km" uniqKey="Carney K">KM Carney</name></author><author><name sortKey="Hungate, Ba" uniqKey="Hungate B">BA Hungate</name></author><author><name sortKey="Drake, Bg" uniqKey="Drake B">BG Drake</name></author><author><name sortKey="Megonigal, Jp" uniqKey="Megonigal J">JP Megonigal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carney, Km" uniqKey="Carney K">KM Carney</name></author><author><name sortKey="Matson, Pa" uniqKey="Matson P">PA 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Farris</name></author><author><name sortKey="Wang, Q" uniqKey="Wang Q">Q Wang</name></author><author><name sortKey="Kulam Syed Mohideen, As" uniqKey="Kulam Syed Mohideen A">AS Kulam-Syed-Mohideen</name></author><author><name sortKey="Mcgarrell, Dm" uniqKey="Mcgarrell D">DM McGarrell</name></author><author><name sortKey="Bandela, Am" uniqKey="Bandela A">AM Bandela</name></author><author><name sortKey="Cardenas, E" uniqKey="Cardenas E">E Cardenas</name></author><author><name sortKey="Garrity, Gm" uniqKey="Garrity G">GM Garrity</name></author><author><name sortKey="Tiedje, Jm" uniqKey="Tiedje J">JM Tiedje</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pruesse, E" uniqKey="Pruesse E">E Pruesse</name></author><author><name sortKey="Quast, C" uniqKey="Quast C">C Quast</name></author><author><name sortKey="Knittel, K" uniqKey="Knittel K">K Knittel</name></author><author><name sortKey="Fuchs, Bm" uniqKey="Fuchs B">BM Fuchs</name></author><author><name sortKey="Ludwig, W" uniqKey="Ludwig W">W Ludwig</name></author><author><name sortKey="Peplies, J" uniqKey="Peplies J">J Peplies</name></author><author><name sortKey="Glockner, Fo" uniqKey="Glockner F">FO Glockner</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Hartman, Amber L" sort="Hartman, Amber L" uniqKey="Hartman A" first="Amber L" last="Hartman">Amber L. Hartman</name></noRegion><name sortKey="Eisen, Jonathan A" sort="Eisen, Jonathan A" uniqKey="Eisen J" first="Jonathan A" last="Eisen">Jonathan A. Eisen</name><name sortKey="Hartman, Amber L" sort="Hartman, Amber L" uniqKey="Hartman A" first="Amber L" last="Hartman">Amber L. Hartman</name><name sortKey="Lud Scher, Bertram" sort="Lud Scher, Bertram" uniqKey="Lud Scher B" first="Bertram" last="Lud Scher">Bertram Lud Scher</name><name sortKey="Mcphillips, Timothy" sort="Mcphillips, Timothy" uniqKey="Mcphillips T" first="Timothy" last="Mcphillips">Timothy Mcphillips</name><name sortKey="Riddle, Sean" sort="Riddle, Sean" uniqKey="Riddle S" first="Sean" last="Riddle">Sean Riddle</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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