MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN]
Identifieur interne : 000383 ( Pmc/Corpus ); précédent : 000382; suivant : 000384MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN]
Auteurs : Michael S. Campbell ; Meiyee Law ; Carson Holt ; Joshua C. Stein ; Gaurav D. Moghe ; David E. Hufnagel ; Jikai Lei ; Rujira Achawanantakun ; Dian Jiao ; Carolyn J. Lawrence ; Doreen Ware ; Shin-Han Shiu ; Kevin L. Childs ; Yanni Sun ; Ning Jiang ; Mark YandellSource :
- Plant Physiology [ 0032-0889 ] ; 2013.
Abstract
Url:
DOI: 10.1104/pp.113.230144
PubMed: 24306534
PubMed Central: 3912085
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations<xref ref-type="author-notes" rid="fn1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn2"><sup>[W]</sup></xref><xref ref-type="author-notes" rid="fn3"><sup>[OPEN]</sup></xref></title><author><name sortKey="Campbell, Michael S" sort="Campbell, Michael S" uniqKey="Campbell M" first="Michael S." last="Campbell">Michael S. Campbell</name></author><author><name sortKey="Law, Meiyee" sort="Law, Meiyee" uniqKey="Law M" first="Meiyee" last="Law">Meiyee Law</name></author><author><name sortKey="Holt, Carson" sort="Holt, Carson" uniqKey="Holt C" first="Carson" last="Holt">Carson Holt</name></author><author><name sortKey="Stein, Joshua C" sort="Stein, Joshua C" uniqKey="Stein J" first="Joshua C." last="Stein">Joshua C. Stein</name></author><author><name sortKey="Moghe, Gaurav D" sort="Moghe, Gaurav D" uniqKey="Moghe G" first="Gaurav D." last="Moghe">Gaurav D. Moghe</name></author><author><name sortKey="Hufnagel, David E" sort="Hufnagel, David E" uniqKey="Hufnagel D" first="David E." last="Hufnagel">David E. Hufnagel</name></author><author><name sortKey="Lei, Jikai" sort="Lei, Jikai" uniqKey="Lei J" first="Jikai" last="Lei">Jikai Lei</name></author><author><name sortKey="Achawanantakun, Rujira" sort="Achawanantakun, Rujira" uniqKey="Achawanantakun R" first="Rujira" last="Achawanantakun">Rujira Achawanantakun</name></author><author><name sortKey="Jiao, Dian" sort="Jiao, Dian" uniqKey="Jiao D" first="Dian" last="Jiao">Dian Jiao</name></author><author><name sortKey="Lawrence, Carolyn J" sort="Lawrence, Carolyn J" uniqKey="Lawrence C" first="Carolyn J." last="Lawrence">Carolyn J. Lawrence</name></author><author><name sortKey="Ware, Doreen" sort="Ware, Doreen" uniqKey="Ware D" first="Doreen" last="Ware">Doreen Ware</name></author><author><name sortKey="Shiu, Shin Han" sort="Shiu, Shin Han" uniqKey="Shiu S" first="Shin-Han" last="Shiu">Shin-Han Shiu</name></author><author><name sortKey="Childs, Kevin L" sort="Childs, Kevin L" uniqKey="Childs K" first="Kevin L." last="Childs">Kevin L. Childs</name></author><author><name sortKey="Sun, Yanni" sort="Sun, Yanni" uniqKey="Sun Y" first="Yanni" last="Sun">Yanni Sun</name></author><author><name sortKey="Jiang, Ning" sort="Jiang, Ning" uniqKey="Jiang N" first="Ning" last="Jiang">Ning Jiang</name></author><author><name sortKey="Yandell, Mark" sort="Yandell, Mark" uniqKey="Yandell M" first="Mark" last="Yandell">Mark Yandell</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24306534</idno><idno type="pmc">3912085</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912085</idno><idno type="RBID">PMC:3912085</idno><idno type="doi">10.1104/pp.113.230144</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000383</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations<xref ref-type="author-notes" rid="fn1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn2"><sup>[W]</sup></xref><xref ref-type="author-notes" rid="fn3"><sup>[OPEN]</sup></xref></title><author><name sortKey="Campbell, Michael S" sort="Campbell, Michael S" uniqKey="Campbell M" first="Michael S." last="Campbell">Michael S. Campbell</name></author><author><name sortKey="Law, Meiyee" sort="Law, Meiyee" uniqKey="Law M" first="Meiyee" last="Law">Meiyee Law</name></author><author><name sortKey="Holt, Carson" sort="Holt, Carson" uniqKey="Holt C" first="Carson" last="Holt">Carson Holt</name></author><author><name sortKey="Stein, Joshua C" sort="Stein, Joshua C" uniqKey="Stein J" first="Joshua C." last="Stein">Joshua C. Stein</name></author><author><name sortKey="Moghe, Gaurav D" sort="Moghe, Gaurav D" uniqKey="Moghe G" first="Gaurav D." last="Moghe">Gaurav D. Moghe</name></author><author><name sortKey="Hufnagel, David E" sort="Hufnagel, David E" uniqKey="Hufnagel D" first="David E." last="Hufnagel">David E. Hufnagel</name></author><author><name sortKey="Lei, Jikai" sort="Lei, Jikai" uniqKey="Lei J" first="Jikai" last="Lei">Jikai Lei</name></author><author><name sortKey="Achawanantakun, Rujira" sort="Achawanantakun, Rujira" uniqKey="Achawanantakun R" first="Rujira" last="Achawanantakun">Rujira Achawanantakun</name></author><author><name sortKey="Jiao, Dian" sort="Jiao, Dian" uniqKey="Jiao D" first="Dian" last="Jiao">Dian Jiao</name></author><author><name sortKey="Lawrence, Carolyn J" sort="Lawrence, Carolyn J" uniqKey="Lawrence C" first="Carolyn J." last="Lawrence">Carolyn J. Lawrence</name></author><author><name sortKey="Ware, Doreen" sort="Ware, Doreen" uniqKey="Ware D" first="Doreen" last="Ware">Doreen Ware</name></author><author><name sortKey="Shiu, Shin Han" sort="Shiu, Shin Han" uniqKey="Shiu S" first="Shin-Han" last="Shiu">Shin-Han Shiu</name></author><author><name sortKey="Childs, Kevin L" sort="Childs, Kevin L" uniqKey="Childs K" first="Kevin L." last="Childs">Kevin L. Childs</name></author><author><name sortKey="Sun, Yanni" sort="Sun, Yanni" uniqKey="Sun Y" first="Yanni" last="Sun">Yanni Sun</name></author><author><name sortKey="Jiang, Ning" sort="Jiang, Ning" uniqKey="Jiang N" first="Ning" last="Jiang">Ning Jiang</name></author><author><name sortKey="Yandell, Mark" sort="Yandell, Mark" uniqKey="Yandell M" first="Mark" last="Yandell">Mark Yandell</name></author></analytic><series><title level="j">Plant Physiology</title><idno type="ISSN">0032-0889</idno><idno type="eISSN">1532-2548</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>MAKER-P annotates the entire Arabidopsis and maize genomes in less than 3 h with comparable quality to the current TAIR10 and maize V2 annotation builds</italic>.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Plant Physiol</journal-id><journal-id journal-id-type="iso-abbrev">Plant Physiol</journal-id><journal-id journal-id-type="hwp">plantphysiol</journal-id><journal-id journal-id-type="publisher-id">aspb</journal-id><journal-title-group><journal-title>Plant Physiology</journal-title></journal-title-group><issn pub-type="ppub">0032-0889</issn><issn pub-type="epub">1532-2548</issn><publisher><publisher-name>American Society of Plant Biologists</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24306534</article-id><article-id pub-id-type="pmc">3912085</article-id><article-id pub-id-type="publisher-id">230144</article-id><article-id pub-id-type="doi">10.1104/pp.113.230144</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject><subj-group><subject>Breakthrough Technologies</subject></subj-group></subj-group></article-categories><title-group><article-title>MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations<xref ref-type="author-notes" rid="fn1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn2"><sup>[W]</sup></xref><xref ref-type="author-notes" rid="fn3"><sup>[OPEN]</sup></xref></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Campbell</surname><given-names>Michael S.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Law</surname><given-names>MeiYee</given-names></name></contrib><contrib contrib-type="author"><name><surname>Holt</surname><given-names>Carson</given-names></name></contrib><contrib contrib-type="author"><name><surname>Stein</surname><given-names>Joshua C.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Moghe</surname><given-names>Gaurav D.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Hufnagel</surname><given-names>David E.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Lei</surname><given-names>Jikai</given-names></name></contrib><contrib contrib-type="author"><name><surname>Achawanantakun</surname><given-names>Rujira</given-names></name></contrib><contrib contrib-type="author"><name><surname>Jiao</surname><given-names>Dian</given-names></name></contrib><contrib contrib-type="author"><name><surname>Lawrence</surname><given-names>Carolyn J.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Ware</surname><given-names>Doreen</given-names></name></contrib><contrib contrib-type="author"><name><surname>Shiu</surname><given-names>Shin-Han</given-names></name></contrib><contrib contrib-type="author"><name><surname>Childs</surname><given-names>Kevin L.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Sun</surname><given-names>Yanni</given-names></name></contrib><contrib contrib-type="author"><name><surname>Jiang</surname><given-names>Ning</given-names></name></contrib><contrib contrib-type="author"><name><surname>Yandell</surname><given-names>Mark</given-names></name><xref ref-type="corresp" rid="cor1">*</xref></contrib><aff id="aff1">Eccles Institute of Human Genetics (M.S.C., M.L., M.Y.) and Department of Biomedical Informatics (M.L.), University of Utah, Salt Lake City, Utah 84112</aff><aff id="aff2">Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.)</aff><aff id="aff3">Genetics Program (G.D.M., S.-H.S., N.J.), Department of Plant Biology (D.E.H., S.-H.S., K.L.C.), Department of Computer Science and Engineering (R.A., Y.S.), and Department of Horticulture (J.C.S., N.J.), Michigan State University, East Lansing, Michigan 48824</aff><aff id="aff4">University of Texas, Texas Advanced Computing Center, Austin, Texas 78758 (D.J.)</aff><aff id="aff5">United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research Unit and Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011 (C.J.L.)</aff><aff id="aff6">iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (D.W.); and</aff><aff id="aff7">United States Department of Agriculture-Agricultural Research Service North Atlantic Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)</aff></contrib-group><author-notes><fn id="fn1" fn-type="supported-by"><label>1</label><p>This work was supported by the National Science Foundation (grant no. IOS–1126998 to S.-H.S., K.L.C., Y.S., N.J., and M.Y. and grant no. DBI–0735191 to the iPlant Collaborative).</p></fn><corresp id="cor1"><label>*</label>Address correspondence to <email>myandell@genetics.utah.edu</email>.</corresp><fn id="afn1"><p>The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (<ext-link ext-link-type="uri" xlink:href="http://www.plantphysiol.org">www.plantphysiol.org</ext-link>) is: Mark Yandell (<email>myandell@genetics.utah.edu</email>).</p></fn><fn id="fn2"><label>[W]</label><p>The online version of this article contains Web-only data.</p></fn><fn id="fn3"><label>[OPEN]</label><p>Articles can be viewed online without a subscription.</p></fn><fn><p><ext-link ext-link-type="uri" xlink:href="http://www.plantphysiol.org/cgi/doi/10.1104/pp.113.230144">www.plantphysiol.org/cgi/doi/10.1104/pp.113.230144</ext-link></p></fn></author-notes><pmc-comment>Fake ppub date generated by PMC from publisher
pub-date/@pub-type='epub-ppub' </pmc-comment>
<pub-date pub-type="ppub"><month>2</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>04</day><month>12</month><year>2013</year></pub-date><pub-date pub-type="pmc-release"><day>04</day><month>12</month><year>2013</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>164</volume><issue>2</issue><fpage>513</fpage><lpage>524</lpage><history><date date-type="received"><day>08</day><month>10</month><year>2013</year></date><date date-type="accepted"><day>26</day><month>11</month><year>2013</year></date></history><permissions><copyright-statement>© 2014 American Society of Plant Biologists. All Rights Reserved.</copyright-statement><copyright-year>2014</copyright-year></permissions><self-uri xlink:role="icon" xlink:type="simple" xlink:href="PP_230144_ic1.gif"></self-uri><self-uri content-type="alt-lang-pdf zh" xlink:type="simple" xlink:href="513.chinese.pdf"></self-uri><abstract abstract-type="precis"><p><italic>MAKER-P annotates the entire Arabidopsis and maize genomes in less than 3 h with comparable quality to the current TAIR10 and maize V2 annotation builds</italic>.</p></abstract><abstract><p>We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. We have benchmarked the resulting software tool kit, MAKER-P, using the Arabidopsis (<italic>Arabidopsis thaliana</italic>) and maize (<italic>Zea mays</italic>) genomes. Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER-P on the Texas Advanced Computing Center. We show that this public resource can de novo annotate the entire Arabidopsis and maize genomes in less than 3 h and produce annotations of comparable quality to those of the current The Arabidopsis Information Resource 10 and maize V2 annotation builds.</p></abstract><counts><page-count count="12"></page-count></counts></article-meta><notes><glossary><title>Glossary</title><def-list><def-item><term id="term1">ncRNA</term><def id="def1"><p>noncoding RNA</p></def></def-item><def-item><term id="term2">TACC</term><def id="def2"><p>Texas Advanced Computing Center</p></def></def-item><def-item><term id="term3">TAIR10</term><def id="def3"><p>The Arabidopsis Information Resource 10</p></def></def-item><def-item><term id="term4">cDNA</term><def id="def4"><p>complementary DNA</p></def></def-item><def-item><term id="term5">TAIR</term><def id="def5"><p>The Arabidopsis Information Resource</p></def></def-item><def-item><term id="term6">AED</term><def id="def6"><p>Annotation Edit Distance</p></def></def-item><def-item><term id="term7">CDF</term><def id="def7"><p>cumulative distribution function</p></def></def-item><def-item><term id="term8">UTR</term><def id="def8"><p>untranslated region</p></def></def-item><def-item><term id="term9">miRNA</term><def id="def9"><p>microRNA</p></def></def-item><def-item><term id="term10">CPUs</term><def id="def10"><p>central processing units</p></def></def-item><def-item><term id="term11">NCBI</term><def id="def11"><p>National Center for Biotechnology Information</p></def></def-item></def-list></glossary></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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