MEGANTE: A Web-Based System for Integrated Plant Genome Annotation
Identifieur interne : 000647 ( Pmc/Curation ); précédent : 000646; suivant : 000648MEGANTE: A Web-Based System for Integrated Plant Genome Annotation
Auteurs : Hisataka Numa ; Takeshi ItohSource :
- Plant and Cell Physiology [ 0032-0781 ] ; 2013.
Abstract
The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable increase in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this process requires substantial expertise and knowledge of bioinformatics. Here we present MEGANTE, a web-based annotation system that makes plant genome annotation easy for researchers unfamiliar with bioinformatics. Without any complicated configuration, users can perform genomic sequence annotations simply by uploading a sequence and selecting the species to query. MEGANTE automatically runs several analysis programs and integrates the results to select the appropriate consensus exon–intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation, including a similarity search against known proteins and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with a widely used genome browser, GBrowse. For ease of analysis, the results can be downloaded in Microsoft Excel format. All of the query sequences and annotation results are stored on the server side so that users can access their own data from virtually anywhere on the web. The current release of MEGANTE targets 24 plant species from the
Url:
DOI: 10.1093/pcp/pct157
PubMed: 24253915
PubMed Central: 3894707
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<author><name sortKey="Itoh, Takeshi" sort="Itoh, Takeshi" uniqKey="Itoh T" first="Takeshi" last="Itoh">Takeshi Itoh</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">MEGANTE: A Web-Based System for Integrated Plant Genome Annotation</title>
<author><name sortKey="Numa, Hisataka" sort="Numa, Hisataka" uniqKey="Numa H" first="Hisataka" last="Numa">Hisataka Numa</name>
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<author><name sortKey="Itoh, Takeshi" sort="Itoh, Takeshi" uniqKey="Itoh T" first="Takeshi" last="Itoh">Takeshi Itoh</name>
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<series><title level="j">Plant and Cell Physiology</title>
<idno type="ISSN">0032-0781</idno>
<idno type="eISSN">1471-9053</idno>
<imprint><date when="2013">2013</date>
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<front><div type="abstract" xml:lang="en"><p>The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable increase in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this process requires substantial expertise and knowledge of bioinformatics. Here we present MEGANTE, a web-based annotation system that makes plant genome annotation easy for researchers unfamiliar with bioinformatics. Without any complicated configuration, users can perform genomic sequence annotations simply by uploading a sequence and selecting the species to query. MEGANTE automatically runs several analysis programs and integrates the results to select the appropriate consensus exon–intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation, including a similarity search against known proteins and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with a widely used genome browser, GBrowse. For ease of analysis, the results can be downloaded in Microsoft Excel format. All of the query sequences and annotation results are stored on the server side so that users can access their own data from virtually anywhere on the web. The current release of MEGANTE targets 24 plant species from the <italic>Brassicaceae</italic>
, <italic>Fabaceae</italic>
, <italic>Musaceae</italic>
, <italic>Poaceae</italic>
, <italic>Salicaceae</italic>
, <italic>Solanaceae</italic>
, <italic>Rosaceae</italic>
and <italic>Vitaceae</italic>
families, and it allows users to submit a sequence up to 10 Mb in length and to save up to 100 sequences with the annotation information on the server. The MEGANTE web service is available at <ext-link ext-link-type="uri" xlink:href="https://megante.dna.affrc.go.jp/">https://megante.dna.affrc.go.jp/</ext-link>
.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Plant Cell Physiol</journal-id>
<journal-id journal-id-type="iso-abbrev">Plant Cell Physiol</journal-id>
<journal-id journal-id-type="publisher-id">pcp</journal-id>
<journal-id journal-id-type="hwp">pcellphys</journal-id>
<journal-title-group><journal-title>Plant and Cell Physiology</journal-title>
</journal-title-group>
<issn pub-type="ppub">0032-0781</issn>
<issn pub-type="epub">1471-9053</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24253915</article-id>
<article-id pub-id-type="pmc">3894707</article-id>
<article-id pub-id-type="doi">10.1093/pcp/pct157</article-id>
<article-id pub-id-type="publisher-id">pct157</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Special Online Collection – Database Papers</subject>
</subj-group>
</article-categories>
<title-group><article-title>MEGANTE: A Web-Based System for Integrated Plant Genome Annotation</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Numa</surname>
<given-names>Hisataka</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Itoh</surname>
<given-names>Takeshi</given-names>
</name>
<xref ref-type="corresp" rid="pct157-COR1">*</xref>
</contrib>
<aff>Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan</aff>
</contrib-group>
<author-notes><corresp id="pct157-COR1">*Corresponding author: E-mail, <email>taitoh@affrc.go.jp</email>
; Fax, <fax>+81-29-838-7065</fax>
.</corresp>
</author-notes>
<pub-date pub-type="ppub"><month>1</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>17</day>
<month>12</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>17</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
. </pmc-comment>
<volume>55</volume>
<issue>1</issue>
<fpage>e2</fpage>
<lpage>e2</lpage>
<history><date date-type="received"><day>21</day>
<month>8</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>18</day>
<month>10</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-statement>© The Author 2013. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.</copyright-statement>
<copyright-year>2013</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/3.0/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/3.0/">http://creativecommons.org/licenses/by-nc/3.0/</ext-link>
), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com</license-p>
</license>
</permissions>
<abstract><p>The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable increase in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this process requires substantial expertise and knowledge of bioinformatics. Here we present MEGANTE, a web-based annotation system that makes plant genome annotation easy for researchers unfamiliar with bioinformatics. Without any complicated configuration, users can perform genomic sequence annotations simply by uploading a sequence and selecting the species to query. MEGANTE automatically runs several analysis programs and integrates the results to select the appropriate consensus exon–intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation, including a similarity search against known proteins and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with a widely used genome browser, GBrowse. For ease of analysis, the results can be downloaded in Microsoft Excel format. All of the query sequences and annotation results are stored on the server side so that users can access their own data from virtually anywhere on the web. The current release of MEGANTE targets 24 plant species from the <italic>Brassicaceae</italic>
, <italic>Fabaceae</italic>
, <italic>Musaceae</italic>
, <italic>Poaceae</italic>
, <italic>Salicaceae</italic>
, <italic>Solanaceae</italic>
, <italic>Rosaceae</italic>
and <italic>Vitaceae</italic>
families, and it allows users to submit a sequence up to 10 Mb in length and to save up to 100 sequences with the annotation information on the server. The MEGANTE web service is available at <ext-link ext-link-type="uri" xlink:href="https://megante.dna.affrc.go.jp/">https://megante.dna.affrc.go.jp/</ext-link>
.</p>
</abstract>
<kwd-group><kwd>Gene prediction</kwd>
<kwd>Plant genome annotation</kwd>
<kwd>Web service</kwd>
</kwd-group>
<counts><page-count count="8"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
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