Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding
Identifieur interne : 000667 ( Pmc/Checkpoint ); précédent : 000666; suivant : 000668Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding
Auteurs : Wayne K. Dawson ; Kazuya Fujiwara ; Gota KawaiSource :
- PLoS ONE [ 1932-6203 ] ; 2007.
Abstract
Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem. Yet neglecting pseudoknots limits the utility of such approaches. Here, an algorithm utilizing structure mapping and thermodynamics is introduced for RNA pseudoknot prediction that finds the minimum free energy and identifies information about the flexibility of the RNA. The heuristic approach takes advantage of the 5′ to 3′ folding direction of many biological RNA molecules and is consistent with the hierarchical folding hypothesis and the contact order model. Mapping methods are used to build and analyze the folded structure for pseudoknots and to add important 3D structural considerations. The program can predict some well known pseudoknot structures correctly. The results of this study suggest that many functional RNA sequences are optimized for proper folding. They also suggest directions we can proceed in the future to achieve even better results.
Url:
DOI: 10.1371/journal.pone.0000905
PubMed: 17878940
PubMed Central: 1975678
Affiliations:
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<front><div type="abstract" xml:lang="en"><p>Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem. Yet neglecting pseudoknots limits the utility of such approaches. Here, an algorithm utilizing structure mapping and thermodynamics is introduced for RNA pseudoknot prediction that finds the minimum free energy and identifies information about the flexibility of the RNA. The heuristic approach takes advantage of the 5′ to 3′ folding direction of many biological RNA molecules and is consistent with the hierarchical folding hypothesis and the contact order model. Mapping methods are used to build and analyze the folded structure for pseudoknots and to add important 3D structural considerations. The program can predict some well known pseudoknot structures correctly. The results of this study suggest that many functional RNA sequences are optimized for proper folding. They also suggest directions we can proceed in the future to achieve even better results.</p>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
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<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
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</journal-meta>
<article-meta><article-id pub-id-type="pmid">17878940</article-id>
<article-id pub-id-type="pmc">1975678</article-id>
<article-id pub-id-type="publisher-id">07-PONE-RA-01595R1</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0000905</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline"><subject>Biophysics</subject>
<subject>Biophysics/Protein Folding</subject>
<subject>Biophysics/RNA Structure</subject>
<subject>Biophysics/Theory and Simulation</subject>
<subject>Biotechnology/Bioengineering</subject>
<subject>Computational Biology/Evolutionary Modeling</subject>
</subj-group>
</article-categories>
<title-group><article-title>Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding</article-title>
<alt-title alt-title-type="running-head">RNA Pseudoknot Prediction</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Dawson</surname>
<given-names>Wayne K.</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
<xref ref-type="corresp" rid="n101"><sup>*</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Fujiwara</surname>
<given-names>Kazuya</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kawai</surname>
<given-names>Gota</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
</contrib-group>
<aff id="aff1"><addr-line>Department of Life and Environmental Sciences, Chiba Institute of Technology, Narashino-shi, Chiba, Japan</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Egli</surname>
<given-names>Martin</given-names>
</name>
<role>Academic Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">Vanderbilt University, United States of America</aff>
<author-notes><corresp id="n101">* To whom correspondence should be addressed. E-mail: <email>wayne.dawson@it-chiba.ac.jp</email>
</corresp>
<fn fn-type="con"><p>Conceived and designed the experiments: WD. Performed the experiments: WD. Analyzed the data: WD. Contributed reagents/materials/analysis tools: KF GK. Wrote the paper: WD. Other: Helped extensively in building the web interface: KF. Helped extensively in making the graphics able to display pseudoknots: KF. Contributed to preparing the manuscript: GK. Advised on research matters: GK. Contributed experimental information: GK. Contributed some of the referenced literature/database information: GK. Designed and wrote the majority of the c++program (∼40000 lines with pseudogenes and SINEs): WD. Discovered and developed the concepts of this theory: WD. Carried out most of the literature study and analysis: WD.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2007</year>
</pub-date>
<pub-date pub-type="epub"><day>19</day>
<month>9</month>
<year>2007</year>
</pub-date>
<volume>2</volume>
<issue>9</issue>
<elocation-id>e905</elocation-id>
<history><date date-type="received"><day>26</day>
<month>6</month>
<year>2007</year>
</date>
<date date-type="accepted"><day>8</day>
<month>8</month>
<year>2007</year>
</date>
</history>
<permissions><copyright-statement>Dawson et al.</copyright-statement>
<copyright-year>2007</copyright-year>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p>
</license>
</permissions>
<abstract><p>Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem. Yet neglecting pseudoknots limits the utility of such approaches. Here, an algorithm utilizing structure mapping and thermodynamics is introduced for RNA pseudoknot prediction that finds the minimum free energy and identifies information about the flexibility of the RNA. The heuristic approach takes advantage of the 5′ to 3′ folding direction of many biological RNA molecules and is consistent with the hierarchical folding hypothesis and the contact order model. Mapping methods are used to build and analyze the folded structure for pseudoknots and to add important 3D structural considerations. The program can predict some well known pseudoknot structures correctly. The results of this study suggest that many functional RNA sequences are optimized for proper folding. They also suggest directions we can proceed in the future to achieve even better results.</p>
</abstract>
<counts><page-count count="7"></page-count>
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<tree><noCountry><name sortKey="Dawson, Wayne K" sort="Dawson, Wayne K" uniqKey="Dawson W" first="Wayne K." last="Dawson">Wayne K. Dawson</name>
<name sortKey="Fujiwara, Kazuya" sort="Fujiwara, Kazuya" uniqKey="Fujiwara K" first="Kazuya" last="Fujiwara">Kazuya Fujiwara</name>
<name sortKey="Kawai, Gota" sort="Kawai, Gota" uniqKey="Kawai G" first="Gota" last="Kawai">Gota Kawai</name>
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