A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures
Identifieur interne : 001193 ( Main/Exploration ); précédent : 001192; suivant : 001194A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures
Auteurs : Hosna Jabbari ; Anne CondonSource :
- BMC Bioinformatics [ 1471-2105 ] ; 2014.
Abstract
Improving accuracy and efficiency of computational methods that predict pseudoknotted RNA secondary structures is an ongoing challenge. Existing methods based on free energy minimization tend to be very slow and are limited in the types of pseudoknots that they can predict. Incorporating known structural information can improve prediction accuracy; however, there are not many methods for prediction of pseudoknotted structures that can incorporate structural information as input. There is even less understanding of the relative robustness of these methods with respect to partial information.
We present a new method, Iterative HFold, for pseudoknotted RNA secondary structure prediction. Iterative HFold takes as input a pseudoknot-free structure, and produces a possibly pseudoknotted structure whose energy is at least as low as that of any (density-2) pseudoknotted structure containing the input structure. Iterative HFold leverages strengths of earlier methods, namely the fast running time of HFold, a method that is based on the hierarchical folding hypothesis, and the energy parameters of HotKnots V2.0.
Our experimental evaluation on a large data set shows that Iterative HFold is robust with respect to partial information, with average accuracy on pseudoknotted structures steadily increasing from roughly 54% to 79% as the user provides up to 40% of the input structure.
Iterative HFold is much faster than HotKnots V2.0, while having comparable accuracy. Iterative HFold also has significantly better accuracy than IPknot on our HK-PK and IP-pk168 data sets.
Iterative HFold is a robust method for prediction of pseudoknotted RNA secondary structures, whose accuracy with more than 5% information about true pseudoknot-free structures is better than that of IPknot, and with about 35% information about true pseudoknot-free structures compares well with that of HotKnots V2.0 while being significantly faster. Iterative HFold and all data used in this work are freely available at
The online version of this article (doi:10.1186/1471-2105-15-147) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2105-15-147
PubMed: 24884954
PubMed Central: 4064103
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures</title><author><name sortKey="Jabbari, Hosna" sort="Jabbari, Hosna" uniqKey="Jabbari H" first="Hosna" last="Jabbari">Hosna Jabbari</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author><author><name sortKey="Condon, Anne" sort="Condon, Anne" uniqKey="Condon A" first="Anne" last="Condon">Anne Condon</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24884954</idno><idno type="pmc">4064103</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064103</idno><idno type="RBID">PMC:4064103</idno><idno type="doi">10.1186/1471-2105-15-147</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000192</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000192</idno><idno type="wicri:Area/Pmc/Curation">000192</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000192</idno><idno type="wicri:Area/Pmc/Checkpoint">000661</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000661</idno><idno type="wicri:Area/Ncbi/Merge">000445</idno><idno type="wicri:Area/Ncbi/Curation">000445</idno><idno type="wicri:Area/Ncbi/Checkpoint">000445</idno><idno type="wicri:Area/Main/Merge">001195</idno><idno type="wicri:Area/Main/Curation">001193</idno><idno type="wicri:Area/Main/Exploration">001193</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures</title><author><name sortKey="Jabbari, Hosna" sort="Jabbari, Hosna" uniqKey="Jabbari H" first="Hosna" last="Jabbari">Hosna Jabbari</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author><author><name sortKey="Condon, Anne" sort="Condon, Anne" uniqKey="Condon A" first="Anne" last="Condon">Anne Condon</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Improving accuracy and efficiency of computational methods that predict pseudoknotted RNA secondary structures is an ongoing challenge. Existing methods based on free energy minimization tend to be very slow and are limited in the types of pseudoknots that they can predict. Incorporating known structural information can improve prediction accuracy; however, there are not many methods for prediction of pseudoknotted structures that can incorporate structural information as input. There is even less understanding of the relative robustness of these methods with respect to partial information.</p></sec><sec><title>Results</title><p>We present a new method, Iterative HFold, for pseudoknotted RNA secondary structure prediction. Iterative HFold takes as input a pseudoknot-free structure, and produces a possibly pseudoknotted structure whose energy is at least as low as that of any (density-2) pseudoknotted structure containing the input structure. Iterative HFold leverages strengths of earlier methods, namely the fast running time of HFold, a method that is based on the hierarchical folding hypothesis, and the energy parameters of HotKnots V2.0.</p><p>Our experimental evaluation on a large data set shows that Iterative HFold is robust with respect to partial information, with average accuracy on pseudoknotted structures steadily increasing from roughly 54% to 79% as the user provides up to 40% of the input structure.</p><p>Iterative HFold is much faster than HotKnots V2.0, while having comparable accuracy. Iterative HFold also has significantly better accuracy than IPknot on our HK-PK and IP-pk168 data sets.</p></sec><sec><title>Conclusions</title><p>Iterative HFold is a robust method for prediction of pseudoknotted RNA secondary structures, whose accuracy with more than 5% information about true pseudoknot-free structures is better than that of IPknot, and with about 35% information about true pseudoknot-free structures compares well with that of HotKnots V2.0 while being significantly faster. Iterative HFold and all data used in this work are freely available at <ext-link ext-link-type="uri" xlink:href="http://www.cs.ubc.ca/~hjabbari/software.php">http://www.cs.ubc.ca/~hjabbari/software.php</ext-link>.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2105-15-147) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hale, Bj" uniqKey="Hale B">BJ Hale</name></author><author><name sortKey="Yang, C X" uniqKey="Yang C">C-X Yang</name></author><author><name sortKey="Ross, Jw" uniqKey="Ross J">JW Ross</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Deryusheva, S" uniqKey="Deryusheva S">S Deryusheva</name></author><author><name sortKey="Gall, Jg" uniqKey="Gall J">JG Gall</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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uniqKey="Condon A">A Condon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zuker, M" uniqKey="Zuker M">M Zuker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bellaousov, S" uniqKey="Bellaousov S">S Bellaousov</name></author><author><name sortKey="Mathews, Dh" uniqKey="Mathews D">DH Mathews</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nethercote, N" uniqKey="Nethercote N">N Nethercote</name></author><author><name sortKey="Seward, J" uniqKey="Seward J">J Seward</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Condon, Anne" sort="Condon, Anne" uniqKey="Condon A" first="Anne" last="Condon">Anne Condon</name><name sortKey="Jabbari, Hosna" sort="Jabbari, Hosna" uniqKey="Jabbari H" first="Hosna" last="Jabbari">Hosna Jabbari</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous 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