CovidV1, Ncbi, Checkpoint, bibRecord, 000406

The RNA shapes studio

Identifieur interne : 000406 ( Ncbi/Checkpoint ); précédent : 000405; suivant : 000407

The RNA shapes studio

Auteurs : Stefan Janssen ; Robert Giegerich

Source :

Bioinformatics [ 1367-4803 ] ; 2014.

RBID : PMC:4308662

Abstract

Motivation: 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.

Results: We have rebuilt the original RNAshapes as a repository of components that allows us to integrate several established tools for RNA structure analysis: RNAshapes, RNAalishapes and pknotsRG, including its recent extension pKiss. As a spin-off, we obtain heretofore unavailable functionality: e. g. with pKiss, we can now perform abstract shape analysis for structures holding pseudoknots up to the complexity of kissing hairpin motifs. The new tool pAliKiss can predict kissing hairpin motifs from aligned sequences. Along with the integration, the functionality of the tools was also extended in manifold ways.

Availability and implementation: As before, the tool is available on the Bielefeld Bioinformatics server at http://bibiserv.cebitec.uni-bielefeld.de/rnashapesstudio.

Contact: bibi-help@cebitec.uni-bielefeld.de

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4308662

DOI: 10.1093/bioinformatics/btu649
PubMed: 25273103
PubMed Central: 4308662

Affiliations:

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PMC:4308662

Le document en format XML

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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>
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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>
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: <email>bibi-help@cebitec.uni-bielefeld.de</email>
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The RNA shapes studio

The RNA shapes studio

Source :

Abstract

Links toward previous steps (curation, corpus...)

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

Pour générer des pages wiki