The RNA shapes studio
Identifieur interne : 000A03 ( Main/Exploration ); précédent : 000A02; suivant : 000A04The RNA shapes studio
Auteurs : Stefan Janssen ; Robert GiegerichSource :
- Bioinformatics [ 1367-4803 ] ; 2014.
Abstract
Url:
DOI: 10.1093/bioinformatics/btu649
PubMed: 25273103
PubMed Central: 4308662
Affiliations:
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Le document en format XML
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<author><name sortKey="Janssen, Stefan" sort="Janssen, Stefan" uniqKey="Janssen S" first="Stefan" last="Janssen">Stefan Janssen</name>
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<author><name sortKey="Giegerich, Robert" sort="Giegerich, Robert" uniqKey="Giegerich R" first="Robert" last="Giegerich">Robert Giegerich</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The RNA shapes studio</title>
<author><name sortKey="Janssen, Stefan" sort="Janssen, Stefan" uniqKey="Janssen S" first="Stefan" last="Janssen">Stefan Janssen</name>
</author>
<author><name sortKey="Giegerich, Robert" sort="Giegerich, Robert" uniqKey="Giegerich R" first="Robert" last="Giegerich">Robert Giegerich</name>
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<series><title level="j">Bioinformatics</title>
<idno type="ISSN">1367-4803</idno>
<idno type="eISSN">1367-4811</idno>
<imprint><date when="2014">2014</date>
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<front><div type="abstract" xml:lang="en"><p><bold>Motivation</bold>
: Abstract shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable to focusing in a single structure of minimal free energy. We report recent extensions to this approach.</p>
<p><bold>Results</bold>
: We have rebuilt the original RNA<sc>shapes</sc>
as a repository of components that allows us to integrate several established tools for RNA structure analysis: RNA<sc>shapes</sc>
, RNA<sc>alishapes</sc>
and <sc>pknots</sc>
RG, including its recent extension <sc>p</sc>
K<sc>iss</sc>
. As a spin-off, we obtain heretofore unavailable functionality: e. g. with <sc>p</sc>
K<sc>iss</sc>
, we can now perform abstract shape analysis for structures holding pseudoknots up to the complexity of kissing hairpin motifs. The new tool <sc>p</sc>
A<sc>li</sc>
K<sc>iss</sc>
can predict kissing hairpin motifs from aligned sequences. Along with the integration, the functionality of the tools was also extended in manifold ways.</p>
<p><bold>Availability and implementation</bold>
: As before, the tool is available on the Bielefeld Bioinformatics server at <ext-link ext-link-type="uri" xlink:href="http://bibiserv.cebitec.uni-bielefeld.de/rnashapesstudio">http://bibiserv.cebitec.uni-bielefeld.de/rnashapesstudio</ext-link>
.</p>
<p><bold>Contact</bold>
: <email>bibi-help@cebitec.uni-bielefeld.de</email>
</p>
</div>
</front>
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<biblStruct><analytic><author><name sortKey="Bernhart, S" uniqKey="Bernhart S">S Bernhart</name>
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<biblStruct><analytic><author><name sortKey="Burge, Sw" uniqKey="Burge S">SW Burge</name>
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<biblStruct><analytic><author><name sortKey="Darty, K" uniqKey="Darty K">K Darty</name>
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<biblStruct><analytic><author><name sortKey="Giegerich, R" uniqKey="Giegerich R">R Giegerich</name>
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<biblStruct><analytic><author><name sortKey="Giegerich, R" uniqKey="Giegerich R">R Giegerich</name>
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<biblStruct><analytic><author><name sortKey="Janssen, S" uniqKey="Janssen S">S Janssen</name>
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<biblStruct><analytic><author><name sortKey="Lorenz, R" uniqKey="Lorenz R">R Lorenz</name>
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<biblStruct><analytic><author><name sortKey="Lu, Zj" uniqKey="Lu Z">ZJ Lu</name>
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<biblStruct><analytic><author><name sortKey="Reeder, J" uniqKey="Reeder J">J Reeder</name>
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<author><name sortKey="Giegerich, R" uniqKey="Giegerich R">R Giegerich</name>
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<biblStruct><analytic><author><name sortKey="Reeder, J" uniqKey="Reeder J">J Reeder</name>
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<author><name sortKey="Giegerich, R" uniqKey="Giegerich R">R Giegerich</name>
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<biblStruct><analytic><author><name sortKey="Reeder, J" uniqKey="Reeder J">J Reeder</name>
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<biblStruct><analytic><author><name sortKey="Reinkensmeier, J" uniqKey="Reinkensmeier J">J Reinkensmeier</name>
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<biblStruct><analytic><author><name sortKey="Sauthoff, G" uniqKey="Sauthoff G">G Sauthoff</name>
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<biblStruct><analytic><author><name sortKey="Steffen, P" uniqKey="Steffen P">P Steffen</name>
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<author><name sortKey="Giegerich, R" uniqKey="Giegerich R">R Giegerich</name>
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<biblStruct><analytic><author><name sortKey="Theis, C" uniqKey="Theis C">C Theis</name>
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<biblStruct><analytic><author><name sortKey="Vo, B" uniqKey="Vo B">B Voß</name>
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<biblStruct><analytic><author><name sortKey="Vo, B" uniqKey="Vo B">B Voß</name>
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<tree><noCountry><name sortKey="Giegerich, Robert" sort="Giegerich, Robert" uniqKey="Giegerich R" first="Robert" last="Giegerich">Robert Giegerich</name>
<name sortKey="Janssen, Stefan" sort="Janssen, Stefan" uniqKey="Janssen S" first="Stefan" last="Janssen">Stefan Janssen</name>
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