De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes
Identifieur interne : 000427 ( Pmc/Checkpoint ); précédent : 000426; suivant : 000428De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes
Auteurs : Christopher A. Gulvik [États-Unis] ; T. Chad Effler [États-Unis] ; Steven W. Wilhelm [États-Unis] ; Alison Buchan [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (
Url:
DOI: 10.1371/journal.pone.0050362
PubMed: 23189198
PubMed Central: 3506598
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes</title><author><name sortKey="Gulvik, Christopher A" sort="Gulvik, Christopher A" uniqKey="Gulvik C" first="Christopher A." last="Gulvik">Christopher A. Gulvik</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, University of Tennessee, Knoxville, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Effler, T Chad" sort="Effler, T Chad" uniqKey="Effler T" first="T. Chad" last="Effler">T. Chad Effler</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, University of Tennessee, Knoxville, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Wilhelm, Steven W" sort="Wilhelm, Steven W" uniqKey="Wilhelm S" first="Steven W." last="Wilhelm">Steven W. Wilhelm</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, University of Tennessee, Knoxville, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Buchan, Alison" sort="Buchan, Alison" uniqKey="Buchan A" first="Alison" last="Buchan">Alison Buchan</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, University of Tennessee, Knoxville, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23189198</idno><idno type="pmc">3506598</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3506598</idno><idno type="RBID">PMC:3506598</idno><idno type="doi">10.1371/journal.pone.0050362</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000614</idno><idno type="wicri:Area/Pmc/Curation">000614</idno><idno type="wicri:Area/Pmc/Checkpoint">000427</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes</title><author><name sortKey="Gulvik, Christopher A" sort="Gulvik, Christopher A" uniqKey="Gulvik C" first="Christopher A." last="Gulvik">Christopher A. Gulvik</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, University of Tennessee, Knoxville, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Effler, T Chad" sort="Effler, T Chad" uniqKey="Effler T" first="T. Chad" last="Effler">T. Chad Effler</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, University of Tennessee, Knoxville, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Wilhelm, Steven W" sort="Wilhelm, Steven W" uniqKey="Wilhelm S" first="Steven W." last="Wilhelm">Steven W. Wilhelm</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, University of Tennessee, Knoxville, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Buchan, Alison" sort="Buchan, Alison" uniqKey="Buchan A" first="Alison" last="Buchan">Alison Buchan</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, University of Tennessee, Knoxville, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (<italic>i.e.,</italic> degeneracies). Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an <italic>in silico</italic> amplification using user defined nucleotide sequence dataset(s) and primer sequences that may contain degenerate bases. The program returns an output file that contains the <italic>in silico</italic> amplicons. When De-MetaST is paired with NCBI’s BLAST (De-MetaST-BLAST), the program also returns the top 10 nr NCBI database hits for each recovered <italic>in silico</italic> amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases, this search tool has potential utility in many data mining applications.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Jarman, Sn" uniqKey="Jarman S">SN Jarman</name></author><author><name sortKey="Deagle, Be" uniqKey="Deagle B">BE Deagle</name></author><author><name sortKey="Gales, Nj" uniqKey="Gales N">NJ Gales</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brown, Mv" uniqKey="Brown M">MV Brown</name></author><author><name sortKey="Schwalbach, Ms" uniqKey="Schwalbach M">MS Schwalbach</name></author><author><name sortKey="Hewson, I" uniqKey="Hewson I">I Hewson</name></author><author><name sortKey="Fuhrman, Ja" uniqKey="Fuhrman J">JA 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23189198</article-id><article-id pub-id-type="pmc">3506598</article-id><article-id pub-id-type="publisher-id">PONE-D-12-17188</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0050362</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis Tools</subject><subject>Metagenomics</subject></subj-group></subj-group><subj-group><subject>Molecular Genetics</subject><subj-group><subject>Gene Identification and Analysis</subject></subj-group></subj-group><subj-group><subject>Biological Data Management</subject><subject>Sequence Analysis</subject></subj-group></subj-group><subj-group><subject>Microbiology</subject><subj-group><subject>Microbial Ecology</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Engineering</subject><subj-group><subject>Signal Processing</subject><subj-group><subject>Data Mining</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title>De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes</article-title><alt-title alt-title-type="running-head">De-MetaST-BLAST: A Primer Validation Tool</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Gulvik</surname><given-names>Christopher A.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Effler</surname><given-names>T. Chad</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wilhelm</surname><given-names>Steven W.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Buchan</surname><given-names>Alison</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Kirchman</surname><given-names>David L.</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>University of Delaware, United States of America</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>abuchan@utk.edu</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: CAG. Performed the experiments: CAG TCE. Analyzed the data: CAG AB. Contributed reagents/materials/analysis tools: AB. Wrote the paper: CAG SWW AB.</p></fn></author-notes><pub-date pub-type="collection"><year>2012</year></pub-date><pub-date pub-type="epub"><day>26</day><month>11</month><year>2012</year></pub-date><volume>7</volume><issue>11</issue><elocation-id>e50362</elocation-id><history><date date-type="received"><day>13</day><month>6</month><year>2012</year></date><date date-type="accepted"><day>24</day><month>10</month><year>2012</year></date></history><permissions><copyright-year>2012</copyright-year><copyright-holder>Gulvik et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><p>Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (<italic>i.e.,</italic> degeneracies). Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an <italic>in silico</italic> amplification using user defined nucleotide sequence dataset(s) and primer sequences that may contain degenerate bases. The program returns an output file that contains the <italic>in silico</italic> amplicons. When De-MetaST is paired with NCBI’s BLAST (De-MetaST-BLAST), the program also returns the top 10 nr NCBI database hits for each recovered <italic>in silico</italic> amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases, this search tool has potential utility in many data mining applications.</p></abstract><funding-group><funding-statement>TCE was supported by an REU award from the National Science Foundation (NSF) (MCB1112001 to SWW). SWW and AB acknowledge NSF award OCE1061352 for support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="7"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Tennessee</li></region></list><tree><country name="États-Unis"><region name="Tennessee"><name sortKey="Gulvik, Christopher A" sort="Gulvik, Christopher A" uniqKey="Gulvik C" first="Christopher A." last="Gulvik">Christopher A. Gulvik</name></region><name sortKey="Buchan, Alison" sort="Buchan, Alison" uniqKey="Buchan A" first="Alison" last="Buchan">Alison Buchan</name><name sortKey="Effler, T Chad" sort="Effler, T Chad" uniqKey="Effler T" first="T. Chad" last="Effler">T. Chad Effler</name><name sortKey="Effler, T Chad" sort="Effler, T Chad" uniqKey="Effler T" first="T. Chad" last="Effler">T. Chad Effler</name><name sortKey="Wilhelm, Steven W" sort="Wilhelm, Steven W" uniqKey="Wilhelm S" first="Steven W." last="Wilhelm">Steven W. Wilhelm</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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