AustralieFrV1, Istex, Corpus, bibRecord, 002075

Mireval: a web tool for simple microRNA prediction in genome sequences

Identifieur interne : 002075 ( Istex/Corpus ); précédent : 002074; suivant : 002076

Mireval: a web tool for simple microRNA prediction in genome sequences

Auteurs : William Ritchie ; François-Xavier Théodule ; Daniel Gautheret

Source :

Bioinformatics [ 1367-4803 ] ; 2008-06-01.

RBID : ISTEX:AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC

Abstract

Summary: We have developed an online tool called mirEval which can search sequences of up to 10 000 nt for novel microRNAs in multiple organisms. It is a comprehensive tool, easy to use and very informative. It will allow users with no prior knowledge of in-silico detection of microRNAs to take advantage of the most successful approaches to investigate sequences of interest. Availability: The mirEval web server is available at http://tagc.univ-mrs.fr/mireval Contact: W.Ritchie@centenary.org.au Supplementary information: Supplementary data are available at Bioinformatics online.

Url:

https://api.istex.fr/document/AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC/fulltext/pdf

DOI: 10.1093/bioinformatics/btn137

Links to Exploration step

ISTEX:AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC

Le document en format XML

<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title>Mireval: a web tool for simple microRNA prediction in genome sequences</title>
<author><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name>
<affiliation><mods:affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</mods:affiliation>
</affiliation>
<affiliation><mods:affiliation>*To whom correspondence should be addressed.</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Theodule, Francois Xavier" sort="Theodule, Francois Xavier" uniqKey="Theodule F" first="François-Xavier" last="Théodule">François-Xavier Théodule</name>
<affiliation><mods:affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Gautheret, Daniel" sort="Gautheret, Daniel" uniqKey="Gautheret D" first="Daniel" last="Gautheret">Daniel Gautheret</name>
<affiliation><mods:affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</mods:affiliation>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">ISTEX</idno>
<idno type="RBID">ISTEX:AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC</idno>
<date when="2008" year="2008">2008</date>
<idno type="doi">10.1093/bioinformatics/btn137</idno>
<idno type="url">https://api.istex.fr/document/AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC/fulltext/pdf</idno>
<idno type="wicri:Area/Istex/Corpus">002075</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">002075</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title level="a">Mireval: a web tool for simple microRNA prediction in genome sequences</title>
<author><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name>
<affiliation><mods:affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</mods:affiliation>
</affiliation>
<affiliation><mods:affiliation>*To whom correspondence should be addressed.</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Theodule, Francois Xavier" sort="Theodule, Francois Xavier" uniqKey="Theodule F" first="François-Xavier" last="Théodule">François-Xavier Théodule</name>
<affiliation><mods:affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Gautheret, Daniel" sort="Gautheret, Daniel" uniqKey="Gautheret D" first="Daniel" last="Gautheret">Daniel Gautheret</name>
<affiliation><mods:affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</mods:affiliation>
</affiliation>
</author>
</analytic>
<monogr></monogr>
<series><title level="j">Bioinformatics</title>
<idno type="ISSN">1367-4803</idno>
<idno type="eISSN">1460-2059</idno>
<imprint><publisher>Oxford University Press</publisher>
<date type="published" when="2008-06-01">2008-06-01</date>
<biblScope unit="volume">24</biblScope>
<biblScope unit="issue">11</biblScope>
<biblScope unit="page" from="1394">1394</biblScope>
<biblScope unit="page" to="1396">1396</biblScope>
</imprint>
<idno type="ISSN">1367-4803</idno>
</series>
</biblStruct>
</sourceDesc>
<seriesStmt><idno type="ISSN">1367-4803</idno>
</seriesStmt>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract">Summary: We have developed an online tool called mirEval which can search sequences of up to 10 000 nt for novel microRNAs in multiple organisms. It is a comprehensive tool, easy to use and very informative. It will allow users with no prior knowledge of in-silico detection of microRNAs to take advantage of the most successful approaches to investigate sequences of interest. Availability: The mirEval web server is available at http://tagc.univ-mrs.fr/mireval Contact: W.Ritchie@centenary.org.au Supplementary information: Supplementary data are available at Bioinformatics online.</div>
</front>
</TEI>
<istex><corpusName>oup</corpusName>
<author><json:item><name>William Ritchie</name>
<affiliations><json:string>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</json:string>
<json:string>*To whom correspondence should be addressed.</json:string>
</affiliations>
</json:item>
<json:item><name>François-Xavier Théodule</name>
<affiliations><json:string>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</json:string>
</affiliations>
</json:item>
<json:item><name>Daniel Gautheret</name>
<affiliations><json:string>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</json:string>
</affiliations>
</json:item>
</author>
<articleId><json:string>btn137</json:string>
</articleId>
<arkIstex>ark:/67375/HXZ-G921M964-W</arkIstex>
<language><json:string>unknown</json:string>
</language>
<originalGenre><json:string>research-article</json:string>
</originalGenre>
<abstract>Summary: We have developed an online tool called mirEval which can search sequences of up to 10 000 nt for novel microRNAs in multiple organisms. It is a comprehensive tool, easy to use and very informative. It will allow users with no prior knowledge of in-silico detection of microRNAs to take advantage of the most successful approaches to investigate sequences of interest. Availability: The mirEval web server is available at http://tagc.univ-mrs.fr/mireval Contact: W.Ritchie@centenary.org.au Supplementary information: Supplementary data are available at Bioinformatics online.</abstract>
<qualityIndicators><score>4.487</score>
<pdfWordCount>1503</pdfWordCount>
<pdfCharCount>9472</pdfCharCount>
<pdfVersion>1.4</pdfVersion>
<pdfPageCount>3</pdfPageCount>
<pdfPageSize>612 x 791 pts</pdfPageSize>
<refBibsNative>true</refBibsNative>
<abstractWordCount>82</abstractWordCount>
<abstractCharCount>584</abstractCharCount>
<keywordCount>0</keywordCount>
</qualityIndicators>
<title>Mireval: a web tool for simple microRNA prediction in genome sequences</title>
<pmid><json:string>18453555</json:string>
</pmid>
<genre><json:string>research-article</json:string>
</genre>
<host><title>Bioinformatics</title>
<language><json:string>unknown</json:string>
</language>
<issn><json:string>1367-4803</json:string>
</issn>
<eissn><json:string>1460-2059</json:string>
</eissn>
<publisherId><json:string>bioinformatics</json:string>
</publisherId>
<volume>24</volume>
<issue>11</issue>
<pages><first>1394</first>
<last>1396</last>
</pages>
<genre><json:string>journal</json:string>
</genre>
<subject><json:item><value>APPLICATIONS NOTES</value>
</json:item>
<json:item><value>GENOME ANALYSIS</value>
</json:item>
</subject>
</host>
<namedEntities><unitex><date><json:string>1000</json:string>
<json:string>2008-05-03</json:string>
</date>
<geogName></geogName>
<orgName><json:string>Oxford University</json:string>
<json:string>France Received</json:string>
</orgName>
<orgName_funder></orgName_funder>
<orgName_provider></orgName_provider>
<persName><json:string>To</json:string>
<json:string>MirEval</json:string>
<json:string>W.Ritchie</json:string>
<json:string>Daniel Gautheret</json:string>
<json:string>Francois-Xavier Theodule</json:string>
</persName>
<placeName><json:string>Australia</json:string>
<json:string>Specificity</json:string>
<json:string>Newtown</json:string>
<json:string>France</json:string>
<json:string>Sydney</json:string>
</placeName>
<ref_url></ref_url>
<ref_bibl><json:string>Griffiths-Jones et al., 2007</json:string>
<json:string>Berezikov et al., 2005</json:string>
<json:string>Flicek et al., 2007</json:string>
<json:string>Tanzer and Stadler, 2006</json:string>
<json:string>Xue et al., 2005</json:string>
<json:string>Hofacker et al., 1994</json:string>
<json:string>Berezikov et al. 2005</json:string>
<json:string>Griffith-Jones et al., 2007</json:string>
<json:string>Cooper et al., 2005</json:string>
<json:string>Jenuth et al., 2000</json:string>
<json:string>Xue et al. (2005)</json:string>
<json:string>Ritchie et al., 2007</json:string>
</ref_bibl>
<bibl></bibl>
</unitex>
</namedEntities>
<ark><json:string>ark:/67375/HXZ-G921M964-W</json:string>
</ark>
<categories><wos><json:string>science</json:string>
<json:string>mathematical & computational biology</json:string>
<json:string>biotechnology & applied microbiology</json:string>
<json:string>biochemical research methods</json:string>
</wos>
<scienceMetrix><json:string>applied sciences</json:string>
<json:string>enabling & strategic technologies</json:string>
<json:string>bioinformatics</json:string>
</scienceMetrix>
<scopus><json:string>1 - Physical Sciences</json:string>
<json:string>2 - Mathematics</json:string>
<json:string>3 - Computational Mathematics</json:string>
<json:string>1 - Physical Sciences</json:string>
<json:string>2 - Computer Science</json:string>
<json:string>3 - Computational Theory and Mathematics</json:string>
<json:string>1 - Physical Sciences</json:string>
<json:string>2 - Computer Science</json:string>
<json:string>3 - Computer Science Applications</json:string>
<json:string>1 - Life Sciences</json:string>
<json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string>
<json:string>3 - Molecular Biology</json:string>
<json:string>1 - Life Sciences</json:string>
<json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string>
<json:string>3 - Biochemistry</json:string>
<json:string>1 - Physical Sciences</json:string>
<json:string>2 - Mathematics</json:string>
<json:string>3 - Statistics and Probability</json:string>
</scopus>
</categories>
<publicationDate>2008</publicationDate>
<copyrightDate>2008</copyrightDate>
<doi><json:string>10.1093/bioinformatics/btn137</json:string>
</doi>
<id>AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC</id>
<score>1</score>
<fulltext><json:item><extension>pdf</extension>
<original>true</original>
<mimetype>application/pdf</mimetype>
<uri>https://api.istex.fr/document/AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC/fulltext/pdf</uri>
</json:item>
<json:item><extension>zip</extension>
<original>false</original>
<mimetype>application/zip</mimetype>
<uri>https://api.istex.fr/document/AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC/fulltext/zip</uri>
</json:item>
<istex:fulltextTEI uri="https://api.istex.fr/document/AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a">Mireval: a web tool for simple microRNA prediction in genome sequences</title>
</titleStmt>
<publicationStmt><authority>ISTEX</authority>
<publisher scheme="https://publisher-list.data.istex.fr">Oxford University Press</publisher>
<availability><licence><p>© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org</p>
</licence>
<p scheme="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-GTWS0RDP-M">oup</p>
</availability>
<date>2008-05-03</date>
</publicationStmt>
<notesStmt><note type="research-article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</note>
<note type="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note>
<note>Associate Editor: Dmitrij Frishman</note>
<note>*To whom correspondence should be addressed.</note>
</notesStmt>
<sourceDesc><biblStruct type="inbook"><analytic><title level="a">Mireval: a web tool for simple microRNA prediction in genome sequences</title>
<author xml:id="author-0000" corresp="yes"><persName><forename type="first">William</forename>
<surname>Ritchie</surname>
</persName>
<affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</affiliation>
<affiliation>*To whom correspondence should be addressed.</affiliation>
</author>
<author xml:id="author-0001"><persName><forename type="first">François-Xavier</forename>
<surname>Théodule</surname>
</persName>
<affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</affiliation>
</author>
<author xml:id="author-0002"><persName><forename type="first">Daniel</forename>
<surname>Gautheret</surname>
</persName>
<affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</affiliation>
</author>
<idno type="istex">AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC</idno>
<idno type="ark">ark:/67375/HXZ-G921M964-W</idno>
<idno type="DOI">10.1093/bioinformatics/btn137</idno>
<idno type="article-id">btn137</idno>
</analytic>
<monogr><title level="j">Bioinformatics</title>
<idno type="pISSN">1367-4803</idno>
<idno type="eISSN">1460-2059</idno>
<idno type="publisher-id">bioinformatics</idno>
<idno type="PublisherID-hwp">bioinfo</idno>
<imprint><publisher>Oxford University Press</publisher>
<date type="published" when="2008-06-01"></date>
<biblScope unit="volume">24</biblScope>
<biblScope unit="issue">11</biblScope>
<biblScope unit="page" from="1394">1394</biblScope>
<biblScope unit="page" to="1396">1396</biblScope>
</imprint>
</monogr>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><creation><date>2008-05-03</date>
</creation>
<abstract><p>Summary: We have developed an online tool called mirEval which can search sequences of up to 10 000 nt for novel microRNAs in multiple organisms. It is a comprehensive tool, easy to use and very informative. It will allow users with no prior knowledge of in-silico detection of microRNAs to take advantage of the most successful approaches to investigate sequences of interest. Availability: The mirEval web server is available at http://tagc.univ-mrs.fr/mireval Contact: W.Ritchie@centenary.org.au Supplementary information: Supplementary data are available at Bioinformatics online.</p>
</abstract>
<textClass><keywords scheme="Journal Subject"><list><head></head>
<item><term>APPLICATIONS NOTES</term>
</item>
</list>
</keywords>
</textClass>
<textClass><keywords scheme="Journal Subject"><list><head></head>
<item><term>GENOME ANALYSIS</term>
</item>
</list>
</keywords>
</textClass>
</profileDesc>
<revisionDesc><change when="2008-05-03">Created</change>
<change when="2008-06-01">Published</change>
</revisionDesc>
</teiHeader>
</istex:fulltextTEI>
<json:item><extension>txt</extension>
<original>false</original>
<mimetype>text/plain</mimetype>
<uri>https://api.istex.fr/document/AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC/fulltext/txt</uri>
</json:item>
</fulltext>
<metadata><istex:metadataXml wicri:clean="corpus oup, element #text not found" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="utf-8"</istex:xmlDeclaration>
<istex:docType PUBLIC="-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" URI="journalpublishing.dtd" name="istex:docType"></istex:docType>
<istex:document><article article-type="research-article">

<front>

<journal-meta>

<journal-id journal-id-type="hwp">bioinfo</journal-id>

<journal-id journal-id-type="publisher-id">bioinformatics</journal-id>

<journal-title>Bioinformatics</journal-title>

<issn pub-type="ppub">1367-4803</issn>

<issn pub-type="epub">1460-2059</issn>

<publisher>

<publisher-name>Oxford University Press</publisher-name>

</publisher>

</journal-meta>

<article-meta>

<article-id pub-id-type="doi">10.1093/bioinformatics/btn137</article-id>

<article-id pub-id-type="publisher-id">btn137</article-id>

<article-categories>

<subj-group>

<subject>APPLICATIONS NOTES</subject>

<subj-group>

<subject>GENOME ANALYSIS</subject>

</subj-group>

</subj-group>

</article-categories>

<title-group>

<article-title>Mireval: a web tool for simple microRNA prediction in genome sequences</article-title>

</title-group>

<contrib-group>

<contrib contrib-type="author" corresp="yes">

<name><surname>Ritchie</surname>
<given-names>William</given-names>
</name>

<xref ref-type="aff" rid="AFF1"><sup>1</sup>
</xref>

<xref ref-type="aff" rid="AFF1"><sup>2</sup>
</xref>

<xref ref-type="corresp" rid="COR1">*</xref>

</contrib>

<contrib contrib-type="author">

<name><surname>Théodule</surname>
<given-names>François-Xavier</given-names>
</name>

<xref ref-type="aff" rid="AFF1"><sup>1</sup>
</xref>

</contrib>

<contrib contrib-type="author">

<name><surname>Gautheret</surname>
<given-names>Daniel</given-names>
</name>

<xref ref-type="aff" rid="AFF1"><sup>3</sup>
</xref>

</contrib>

</contrib-group>

<aff id="AFF1"><sup>1</sup>
INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, <sup>2</sup>
Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and <sup>3</sup>
Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</aff>

<author-notes>

<corresp id="COR1">*To whom correspondence should be addressed.</corresp>

<fn><p>Associate Editor: Dmitrij Frishman</p>
</fn>

</author-notes>

<pub-date pub-type="ppub">

<day>1</day>

<month>6</month>

<year>2008</year>

</pub-date>

<pub-date pub-type="epub">

<day>3</day>

<month>5</month>

<year>2008</year>

</pub-date>

<volume>24</volume>

<issue>11</issue>

<fpage>1394</fpage>

<lpage>1396</lpage>

<history>

<date date-type="received">

<day>25</day>

<month>2</month>

<year>2008</year>

</date>

<date date-type="rev-recd">

<day>10</day>

<month>4</month>

<year>2008</year>

</date>

<date date-type="accepted">

<day>10</day>

<month>4</month>

<year>2008</year>

</date>

</history>

<permissions>

<copyright-statement>© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org</copyright-statement>

<copyright-year>2008</copyright-year>

</permissions>

<abstract>

<p><bold>Summary:</bold>
 We have developed an online tool called mirEval which can search sequences of up to 10 000 nt for novel microRNAs in multiple organisms. It is a comprehensive tool, easy to use and very informative. It will allow users with no prior knowledge of in-silico detection of microRNAs to take advantage of the most successful approaches to investigate sequences of interest.</p>

<p><bold>Availability:</bold>
 The mirEval web server is available at <ext-link ext-link-type="uri" xlink:href="http://tagc.univ-mrs.fr/mireval">http://tagc.univ-mrs.fr/mireval</ext-link>
</p>

<p><bold>Contact:</bold>
 <email>W.Ritchie@centenary.org.au</email>
</p>

<p><bold>Supplementary information:</bold>
 <ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/btn137/DC1">Supplementary data</ext-link>
 are available at <italic>Bioinformatics</italic>
 online.</p>

</abstract>

</article-meta>

</front>

<body>

<sec sec-type="intro" id="SEC1"><title>1 INTRODUCTION</title>

<p>One of the reasons why microRNAs (miRNAs) have avoided our scrutiny for so long is because of their small size (20–22 nt) but also because they lack a common signature in their primary sequence. These two characteristics make miRNAs difficult to detect with classical gene finding algorithms. However, miRNAs can be detected by using characteristics such as the secondary structure and free-folding energy of their precursors, conservation of part of the miRNA sequence or similarity with other miRNAs. These characteristics have been exploited widely in the past years to improve the specificity and sensitivity of miRNA finding algorithm (Berezikov <italic>et al</italic>
. <xref ref-type="bibr" rid="B1">2005</xref>
; Ritchie <italic>et al</italic>
., <xref ref-type="bibr" rid="B7">2007</xref>
; Xue <italic>et al</italic>
., <xref ref-type="bibr" rid="B10">2005</xref>
). However, scientists who have no prior knowledge of how these algorithms work or no computer programming skills may not be able to benefit from up-to-date miRNA detection capabilities.</p>

<p>We have developed a user-friendly online tool called MirEval that allows researchers with no bioinformatics skills to conduct a thorough analysis of an input sequence for novel miRNAs, using four different criteria and with no user-defined cutoff score. MirEval is a useful addition to existing miRNA resources such as miRBase (Griffith-Jones <italic>et al</italic>
., <xref ref-type="bibr" rid="B4">2007</xref>
) that enable similarity searches with known miRNAs.</p>
</sec>

<sec id="SEC2"><title>2 IMPLEMENTATION</title>

<p>MirEval analyses a DNA sequence of up to 10 000 nt based on four criteria that we labeled ‘secondary structure analysis’, ‘conservation analysis’, ‘cluster analysis’ and ‘miRBase BLAST’. Users decide which of these analyses should be carried on and receive a full report that is easy to interpret. Our intent is to provide sufficient information so that users can make an informed choice on the most likely miRNA candidates without imposing an arbitrary scoring system.</p>

<sec id="SEC2.1"><title>2.1 Secondary structure analysis</title>

<p>The Dicer enzyme produces mature miRNAs from precursor hairpin structures. It is this specific hairpin shape that structure-based algorithms search for. MirEval offers two separate structural analysis algorithms that use two different, non-redundant approaches. Input sequences are analyzed with a sliding window of 80 nt at 10 nt steps. Each window is evaluated for stable secondary structures by RNA-fold (Hofacker <italic>et al</italic>
., <xref ref-type="bibr" rid="B5">1994</xref>
) and each hairpin shape (a helix of at least 15 nt with no internal hairpin) is then analyzed as follows.</p>

<p>The first algorithm, ‘Triplet-SVM classifier’ (Xue <italic>et al</italic>
., <xref ref-type="bibr" rid="B10">2005</xref>
), is based on support vector machines (SVM) and takes into account structural and primary sequence elements to classify candidates. It is able to distinguish pre-miRNAs from other hairpin shapes with 90% accuracy. In our implementation, the triplet-SVM classifier was trained on the human set of miRNA precursors taken from miRBase and a negative set extracted from coding regions of the human genome, as described in Xue <italic>et al</italic>
. (<xref ref-type="bibr" rid="B10">2005</xref>
).</p>

<p>The second algorithm was developed in our laboratory and is based solely on structural criteria (Ritchie <italic>et al</italic>
., <xref ref-type="bibr" rid="B7">2007</xref>
). It is efficient in distinguishing miRNA precursors from hairpins that are formed by other ncRNA molecules. It works equally well on human sequences (Sensitivity = 0.8; Specificity = 0.76) and on sequences from more distantly related species (Sensitivity = 0.79; Specificity = 0.75).</p>

<p>Users may select to run either Triplet-SVM or both algorithms. The triplet-SVM classifier is used as the default algorithm because it is faster.</p>
</sec>

<sec id="SEC2.2"><title>2.2 Conservation analysis</title>

<p>Many miRNAs are evolutionary conserved, showing a stronger conservation in the stem of the precursor hairpin than in the loop sequence. This pattern in which a stretch of ∼60 nt is conserved with a drop in conservation towards the middle of the stretch is a characteristic of conserved miRNAs (Berezikov <italic>et al</italic>
., <xref ref-type="bibr" rid="B1">2005</xref>
).</p>

<p>For conservation analysis, mirEval relies on the genomic evolutionary rate profiling (GERP) algorithm (Cooper <italic>et al</italic>
., <xref ref-type="bibr" rid="B2">2005</xref>
). GERP identifies conserved regions and estimates evolutionary rates for individual alignment columns. MirEval uses the pre-calculated GERP scores generated by ENSEMBL on a 10-way alignment of amniota vertebrates (Flicek <italic>et al</italic>
., <xref ref-type="bibr" rid="B3">2007</xref>
). To access this data MirEval performs a Blast alignment of the input sequence on the NCBI ‘Genomes’ databank (Jenuth <italic>et al</italic>
., <xref ref-type="bibr" rid="B6">2000</xref>
) to retrieve the genomic location of the sequence and then downloads the conservation track of this location from ENSEMBL by using the ENSEMBL Perl modules. Currently, the conservation analysis can only be conducted on 10 amniota vertebrates but will extend to other species when these are included in ENSEMBL.</p>
</sec>

<sec id="SEC2.3"><title>2.3 Cluster analysis</title>

<p>miRNAs are often found in genomic clusters. Using this property, Sewer and colleagues (2005) discovered up to 100 novel miRNAs in human, rat and mouse by searching 20 kb genomic regions flanking known miRNAs.</p>

<p>To report on such clustered regions, mirEval first retrieves the genomic position that corresponds to the middle of the input sequence (as described in <xref ref-type="sec" rid="SEC2.2">Section 2.2</xref>
) and retrieves all miRNA elements from the ENSEMBL ncRNA track that lie within a 20 kb flanking region of this position. If three or more known miRNAs are found at this position, MirEval alerts the user by a text message on the output screen.</p>

<p>The ncRNA track at ENSEMBL is directly fed by miRBase (Griffiths-Jones <italic>et al</italic>
., <xref ref-type="bibr" rid="B4">2007</xref>
) through the DAS server system and is therefore always up to date.</p>
</sec>

<sec id="SEC2.4"><title>2.4 miRBase BLAST</title>

<p>Many miRNAs belong to a family of homologous genes (Tanzer and Stadler, <xref ref-type="bibr" rid="B9">2006</xref>
). Therefore, sequence similarity search against a set of known miRNAs is a necessary step in miRNA identification and has been implemented in MirEval.</p>

<p>MirEval reports on sequence similarities between the input sequence and all miRNAs in miRBase by directly submitting Blast requests to the miRBase server. Sequences larger than 1000 nt are first cut up into stretches of 1000 nt with a 100 nt overlap and submitted with a 1 s pause between each submission to reduce load on the miRBase server.</p>
</sec>

<sec id="SEC2.5"><title>2.5 Output and computational issues</title>

<p>MirEval's report is condensed into an easy to read, color-coded output (<xref ref-type="fig" rid="F1">Fig. 1</xref>). This display is essential in evaluating stretches that are likely to be novel miRNAs as overlapping features such as high levels of conservation and a hairpin shaped secondary structure gain more importance when evaluated simultaneously.

<fig id="F1"><label><bold>Fig. 1.</bold>
</label>
<caption><p>Screenshot of MirEval output on a rat genome sequence containing the microRNA rno-miR-1. The italic text indicates that the input sequence is in a microRNA enriched region; the green stretch indicates the presence of a precursor-like hairpin shape; the silver boxes display high scoring hits against miRBase; the yellow/red stretch indicates sequence conservation in 10 amniota genomes (yellow = weak, red = strong conservation).</p>
</caption>
<graphic xlink:href="btn137f1"></graphic>
</fig>
</p>

<p>MirEval is the first miRNA search tool that allows a thorough multi-criteria analysis of input sequences and delivers an unbiased, clear report. One of our main concerns was to ensure that this tool was easy to maintain, long lasting and impervious to version changes. To this end we favored data retrieval methods through connections to stable databases rather than maintaining data locally. This is the case for the ‘conservation analysis’, ‘miRBase BLAST’ and ‘cluster analysis’. The structural analyzes, however, are performed locally but we chose two algorithms that perform well on a wide array of species and that do not need to be retrained on new datasets.</p>

<p>Because MirEval connects to remote databases, runtimes may depend on the accessibility of these databases as well as input sequence length. Longer sequences will require longer Blast searches and larger segments to be retrieved from the ENSEMBL server, therefore adding to the runtime. Runtime for structural analyses varies with sequence length and the number of hairpin shapes in the sequence. We measured runtimes on sets of 100 human sequences with lengths varying between 100 and 10 000 nt (<ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/btn137/DC1">Supplementary Table 1</ext-link>
). Times include client-server transfer, queuing and sequence verification time and are therefore close to what users will experience when using MirEval. Because each analysis uses a different server (two of our own servers for structural analysis and external servers for conservation and clustering), the total runtime is approximately equal to the analysis with the longest runtime, i.e. about 3.5 min for 5 kb.</p>
</sec>

</sec>

</body>

<back>

<ack><title>ACKNOWLEDGEMENTS</title>

<p><italic>Funding</italic>
: This work was supported in part by INCa grant PL0079, ‘microRNA, stem cells and cancer’.</p>

<p><italic>Conflict of Interest</italic>
: none declared.</p>
</ack>

<ref-list><title>REFERENCES</title>

<ref id="B1"><nlm-citation citation-type="journal"><person-group person-group-type="author"><name><surname>Berezikov</surname>
<given-names>E</given-names>
</name>
<etal></etal>
</person-group>
<article-title>Phylogenetic shadowing and computational identification of human microRNA Genes</article-title>
<source>Cell</source>
<year>2005</year>
<volume>120</volume>
<fpage>21</fpage>
<lpage>24</lpage>
</nlm-citation>
</ref>

<ref id="B2"><nlm-citation citation-type="journal"><person-group person-group-type="author"><name><surname>Cooper</surname>
<given-names>GM</given-names>
</name>
<etal></etal>
</person-group>
<article-title>Distribution and intensity of constraint in mammalian genomic sequence</article-title>
<source>Genome Res</source>
<year>2005</year>
<volume>15</volume>
<fpage>901</fpage>
<lpage>913</lpage>
</nlm-citation>
</ref>

<ref id="B3"><nlm-citation citation-type="book"><person-group person-group-type="author"><name><surname>Flicek</surname>
<given-names>P</given-names>
</name>
<etal></etal>
</person-group>
<article-title>Ensembl 2008</article-title>
<source>Nucleic Acids Res.</source>
<year>2007</year>
</nlm-citation>
</ref>

<ref id="B4"><nlm-citation citation-type="book"><person-group person-group-type="author"><name><surname>Griffiths-Jones</surname>
<given-names>S</given-names>
</name>
<etal></etal>
</person-group>
<article-title>miRBase: tools for microRNA genomics</article-title>
<source>Nucleic Acids Res.</source>
<year>2007</year>
</nlm-citation>
</ref>

<ref id="B5"><nlm-citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hofacker</surname>
<given-names>IL</given-names>
</name>
<etal></etal>
</person-group>
<article-title>Fast folding and comparison of RNA secondary structures</article-title>
<source>Monatshefte f Chemie</source>
<year>1994</year>
<volume>125</volume>
<fpage>167</fpage>
<lpage>188</lpage>
</nlm-citation>
</ref>

<ref id="B6"><nlm-citation citation-type="journal"><person-group person-group-type="author"><name><surname>Jenuth</surname>
<given-names>JP</given-names>
</name>
</person-group>
<article-title>The NCBI. publicly available tools and resources on the Web</article-title>
<source>Methods Mol. Biol</source>
<year>2000</year>
<volume>132</volume>
<fpage>301</fpage>
<lpage>312</lpage>
</nlm-citation>
</ref>

<ref id="B7"><nlm-citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ritchie</surname>
<given-names>W</given-names>
</name>
<etal></etal>
</person-group>
<article-title>RNA stem-loops: to be or not to be cleaved by RNAse III</article-title>
<source>RNA</source>
<year>2007</year>
<volume>13</volume>
<fpage>457</fpage>
<lpage>462</lpage>
</nlm-citation>
</ref>

<ref id="B8"><nlm-citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sewer</surname>
<given-names>A</given-names>
</name>
<etal></etal>
</person-group>
<article-title>Identification of clustered microRNAs using an ab initio prediction method</article-title>
<source>BMC Bioinformatics</source>
<year>2005</year>
<volume>6</volume>
<fpage>267</fpage>
</nlm-citation>
</ref>

<ref id="B9"><nlm-citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tanzer</surname>
<given-names>A</given-names>
</name>
<name><surname>Stadler</surname>
<given-names>PF</given-names>
</name>
</person-group>
<article-title>Evolution of microRNAs</article-title>
<source>Methods Mol. Biol</source>
<year>2006</year>
<volume>342</volume>
<fpage>335</fpage>
<lpage>350</lpage>
</nlm-citation>
</ref>

<ref id="B10"><nlm-citation citation-type="journal"><person-group person-group-type="author"><name><surname>Xue</surname>
<given-names>C</given-names>
</name>
<etal></etal>
</person-group>
<article-title>Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine</article-title>
<source>BMC Bioinformatics</source>
<year>2005</year>
<volume>6</volume>
<fpage>310</fpage>
</nlm-citation>
</ref>
</ref-list>

</back>

</article>
</istex:document>
</istex:metadataXml>
<mods version="3.6"><titleInfo><title>Mireval: a web tool for simple microRNA prediction in genome sequences</title>
</titleInfo>
<titleInfo type="alternative" contentType="CDATA"><title>Mireval: a web tool for simple microRNA prediction in genome sequences</title>
</titleInfo>
<name type="personal" displayLabel="corresp"><namePart type="given">William</namePart>
<namePart type="family">Ritchie</namePart>
<affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</affiliation>
<affiliation>*To whom correspondence should be addressed.</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">François-Xavier</namePart>
<namePart type="family">Théodule</namePart>
<affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Daniel</namePart>
<namePart type="family">Gautheret</namePart>
<affiliation>INSERM U928, Technologies Avancées pour le Génome et la Clinique, Luminy Case 906, 13288 Marseille, Cedex 09, France, Centenary Institute, Gene & Stem Cell Therapy Program, Newtown, 2042 Sydney, Australia and Univ Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Bat 400, 91405 Orsay Cedex, France</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<typeOfResource>text</typeOfResource>
<genre type="research-article" displayLabel="research-article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre>
<originInfo><publisher>Oxford University Press</publisher>
<dateIssued encoding="w3cdtf">2008-06-01</dateIssued>
<dateCreated encoding="w3cdtf">2008-05-03</dateCreated>
<copyrightDate encoding="w3cdtf">2008</copyrightDate>
</originInfo>
<abstract>Summary: We have developed an online tool called mirEval which can search sequences of up to 10 000 nt for novel microRNAs in multiple organisms. It is a comprehensive tool, easy to use and very informative. It will allow users with no prior knowledge of in-silico detection of microRNAs to take advantage of the most successful approaches to investigate sequences of interest. Availability: The mirEval web server is available at http://tagc.univ-mrs.fr/mireval Contact: W.Ritchie@centenary.org.au Supplementary information: Supplementary data are available at Bioinformatics online.</abstract>
<note type="footnotes">Associate Editor: Dmitrij Frishman</note>
<note type="author-notes">*To whom correspondence should be addressed.</note>
<relatedItem type="host"><titleInfo><title>Bioinformatics</title>
</titleInfo>
<genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre>
<subject><topic>APPLICATIONS NOTES</topic>
</subject>
<subject><topic>GENOME ANALYSIS</topic>
</subject>
<identifier type="ISSN">1367-4803</identifier>
<identifier type="eISSN">1460-2059</identifier>
<identifier type="PublisherID">bioinformatics</identifier>
<identifier type="PublisherID-hwp">bioinfo</identifier>
<part><date>2008</date>
<detail type="volume"><caption>vol.</caption>
<number>24</number>
</detail>
<detail type="issue"><caption>no.</caption>
<number>11</number>
</detail>
<extent unit="pages"><start>1394</start>
<end>1396</end>
</extent>
</part>
</relatedItem>
<identifier type="istex">AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC</identifier>
<identifier type="DOI">10.1093/bioinformatics/btn137</identifier>
<identifier type="ArticleID">btn137</identifier>
<accessCondition type="use and reproduction" contentType="copyright">© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org</accessCondition>
<recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-GTWS0RDP-M">oup</recordContentSource>
<recordOrigin>© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org</recordOrigin>
</recordInfo>
</mods>
<json:item><extension>json</extension>
<original>false</original>
<mimetype>application/json</mimetype>
<uri>https://api.istex.fr/document/AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC/metadata/json</uri>
</json:item>
</metadata>
<covers><json:item><extension>tiff</extension>
<original>true</original>
<mimetype>image/tiff</mimetype>
<uri>https://api.istex.fr/document/AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC/covers/tiff</uri>
</json:item>
</covers>
<annexes><json:item><extension>jpeg</extension>
<original>true</original>
<mimetype>image/jpeg</mimetype>
<uri>https://api.istex.fr/document/AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC/annexes/jpeg</uri>
</json:item>
<json:item><extension>gif</extension>
<original>true</original>
<mimetype>image/gif</mimetype>
<uri>https://api.istex.fr/document/AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC/annexes/gif</uri>
</json:item>
<json:item><extension>pdf</extension>
<original>true</original>
<mimetype>application/pdf</mimetype>
<uri>https://api.istex.fr/document/AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC/annexes/pdf</uri>
</json:item>
</annexes>
<serie></serie>
</istex>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Wicri/Asie/explor/AustralieFrV1/Data/Istex/Corpus

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002075 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Istex/Corpus/biblio.hfd -nk 002075 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Wicri/Asie
   |area=    AustralieFrV1
   |flux=    Istex
   |étape=   Corpus
   |type=    RBID
   |clé=     ISTEX:AC52E9CF91811FBC6C1FE8AF586DC65BEF7CCFBC
   |texte=   Mireval: a web tool for simple microRNA prediction in genome sequences
}}

This area was generated with Dilib version V0.6.33.
Data generation: Tue Dec 5 10:43:12 2017. Site generation: Tue Mar 5 14:07:20 2024

	Serveur d'exploration sur les relations entre la France et l'Australie
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration sur les relations entre la France et l'Australie

Mireval: a web tool for simple microRNA prediction in genome sequences

Mireval: a web tool for simple microRNA prediction in genome sequences

Source :

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri