RNA Accessibility in cubic time
<p>Abstract</p> <p>Background</p> <p>The accessibility of RNA binding motifs controls the efficacy of many biological processes. Examples are the binding of miRNA, siRNA or bacterial sRNA to their respective targets. Similarly, the accessibility of the Shine-Dalgarno se...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-03-01
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| Series: | Algorithms for Molecular Biology |
| Online Access: | http://www.almob.org/content/6/1/3 |
| _version_ | 1831681007413100544 |
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| author | Hofacker Ivo L Mückstein Ullrike Bernhart Stephan H |
| author_facet | Hofacker Ivo L Mückstein Ullrike Bernhart Stephan H |
| author_sort | Hofacker Ivo L |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The accessibility of RNA binding motifs controls the efficacy of many biological processes. Examples are the binding of miRNA, siRNA or bacterial sRNA to their respective targets. Similarly, the accessibility of the Shine-Dalgarno sequence is essential for translation to start in prokaryotes. Furthermore, many classes of RNA binding proteins require the binding site to be single-stranded.</p> <p>Results</p> <p>We introduce a way to compute the accessibility of all intervals within an RNA sequence in <inline-formula><graphic file="1748-7188-6-3-i1.gif"/></inline-formula>(<it>n</it><sup>3</sup>) time. This improves on previous implementations where only intervals of one defined length were computed in the same time. While the algorithm is in the same efficiency class as sampling approaches, the results, especially if the probabilities get small, are much more exact.</p> <p>Conclusions</p> <p>Our algorithm significantly speeds up methods for the prediction of RNA-RNA interactions and other applications that require the accessibility of RNA molecules. The algorithm is already available in the program RNAplfold of the ViennaRNA package.</p> |
| first_indexed | 2024-12-20T05:48:48Z |
| format | Article |
| id | doaj.art-74e6817965b348eda8528459cd8c9dba |
| institution | Directory Open Access Journal |
| issn | 1748-7188 |
| language | English |
| last_indexed | 2024-12-20T05:48:48Z |
| publishDate | 2011-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Algorithms for Molecular Biology |
| spelling | doaj.art-74e6817965b348eda8528459cd8c9dba2022-12-21T19:51:14ZengBMCAlgorithms for Molecular Biology1748-71882011-03-0161310.1186/1748-7188-6-3RNA Accessibility in cubic timeHofacker Ivo LMückstein UllrikeBernhart Stephan H<p>Abstract</p> <p>Background</p> <p>The accessibility of RNA binding motifs controls the efficacy of many biological processes. Examples are the binding of miRNA, siRNA or bacterial sRNA to their respective targets. Similarly, the accessibility of the Shine-Dalgarno sequence is essential for translation to start in prokaryotes. Furthermore, many classes of RNA binding proteins require the binding site to be single-stranded.</p> <p>Results</p> <p>We introduce a way to compute the accessibility of all intervals within an RNA sequence in <inline-formula><graphic file="1748-7188-6-3-i1.gif"/></inline-formula>(<it>n</it><sup>3</sup>) time. This improves on previous implementations where only intervals of one defined length were computed in the same time. While the algorithm is in the same efficiency class as sampling approaches, the results, especially if the probabilities get small, are much more exact.</p> <p>Conclusions</p> <p>Our algorithm significantly speeds up methods for the prediction of RNA-RNA interactions and other applications that require the accessibility of RNA molecules. The algorithm is already available in the program RNAplfold of the ViennaRNA package.</p>http://www.almob.org/content/6/1/3 |
| spellingShingle | Hofacker Ivo L Mückstein Ullrike Bernhart Stephan H RNA Accessibility in cubic time Algorithms for Molecular Biology |
| title | RNA Accessibility in cubic time |
| title_full | RNA Accessibility in cubic time |
| title_fullStr | RNA Accessibility in cubic time |
| title_full_unstemmed | RNA Accessibility in cubic time |
| title_short | RNA Accessibility in cubic time |
| title_sort | rna accessibility in cubic time |
| url | http://www.almob.org/content/6/1/3 |
| work_keys_str_mv | AT hofackerivol rnaaccessibilityincubictime AT mucksteinullrike rnaaccessibilityincubictime AT bernhartstephanh rnaaccessibilityincubictime |