Fast prediction of RNA-RNA interaction
<p>Abstract</p> <p>Background</p> <p>Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational met...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-01-01
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| Series: | Algorithms for Molecular Biology |
| Online Access: | http://www.almob.org/content/5/1/5 |
| _version_ | 1817967935260459008 |
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| author | Backofen Rolf Salari Raheleh Sahinalp S Cenk |
| author_facet | Backofen Rolf Salari Raheleh Sahinalp S Cenk |
| author_sort | Backofen Rolf |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s). There are a number of algorithms in the literature which can predict a variety of such interactions - unfortunately at a very high computational cost. Although some existing target prediction approaches are much faster, they are specialized for interactions with a single binding site.</p> <p>Methods</p> <p>In this paper we present a novel algorithm to accurately predict the minimum free energy structure of RNA-RNA interaction under the most general type of interactions studied in the literature. Moreover, we introduce a fast heuristic method to predict the specific (multiple) binding sites of two interacting RNAs.</p> <p>Results</p> <p>We verify the performance of our algorithms for joint structure and binding site prediction on a set of known interacting RNA pairs. Experimental results show our algorithms are highly accurate and outperform all competitive approaches.</p> |
| first_indexed | 2024-04-13T12:55:46Z |
| format | Article |
| id | doaj.art-617b0e28e6ca429cb4f2c6a55c85c0bd |
| institution | Directory Open Access Journal |
| issn | 1748-7188 |
| language | English |
| last_indexed | 2024-04-13T12:55:46Z |
| publishDate | 2010-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Algorithms for Molecular Biology |
| spelling | doaj.art-617b0e28e6ca429cb4f2c6a55c85c0bd2022-12-22T02:46:04ZengBMCAlgorithms for Molecular Biology1748-71882010-01-0151510.1186/1748-7188-5-5Fast prediction of RNA-RNA interactionBackofen RolfSalari RahelehSahinalp S Cenk<p>Abstract</p> <p>Background</p> <p>Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s). There are a number of algorithms in the literature which can predict a variety of such interactions - unfortunately at a very high computational cost. Although some existing target prediction approaches are much faster, they are specialized for interactions with a single binding site.</p> <p>Methods</p> <p>In this paper we present a novel algorithm to accurately predict the minimum free energy structure of RNA-RNA interaction under the most general type of interactions studied in the literature. Moreover, we introduce a fast heuristic method to predict the specific (multiple) binding sites of two interacting RNAs.</p> <p>Results</p> <p>We verify the performance of our algorithms for joint structure and binding site prediction on a set of known interacting RNA pairs. Experimental results show our algorithms are highly accurate and outperform all competitive approaches.</p>http://www.almob.org/content/5/1/5 |
| spellingShingle | Backofen Rolf Salari Raheleh Sahinalp S Cenk Fast prediction of RNA-RNA interaction Algorithms for Molecular Biology |
| title | Fast prediction of RNA-RNA interaction |
| title_full | Fast prediction of RNA-RNA interaction |
| title_fullStr | Fast prediction of RNA-RNA interaction |
| title_full_unstemmed | Fast prediction of RNA-RNA interaction |
| title_short | Fast prediction of RNA-RNA interaction |
| title_sort | fast prediction of rna rna interaction |
| url | http://www.almob.org/content/5/1/5 |
| work_keys_str_mv | AT backofenrolf fastpredictionofrnarnainteraction AT salariraheleh fastpredictionofrnarnainteraction AT sahinalpscenk fastpredictionofrnarnainteraction |