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- Publisher Website: 10.1007/978-3-319-19048-8_18
- Scopus: eid_2-s2.0-84944527480
- WOS: WOS:000362026100018
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Conference Paper: Predicting RNA secondary structures: one-grammar-fits-all solution
Title | Predicting RNA secondary structures: one-grammar-fits-all solution |
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Authors | |
Issue Date | 2015 |
Publisher | Springer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/ |
Citation | The 11th International Symposium on Bioinformatics Research and Applications (ISBRA 2015), Norfolk, VA., 7-10 June 2015. In Lecture Notes in Computer Science, 2015, v. 9096, p. 211-222 How to Cite? |
Abstract | RNA secondary structures are known to be important in many biological processes. Many available programs have been developed for RNA secondary structure prediction. Based on our knowledge, however, there still exist secondary structures of known RNA sequences which cannot be covered by these algorithms. In this paper, we provide an efficient algorithm that can handle all RNA secondary structures found in Rfam database. We designed a new stochastic context-free grammar named Rectangle Tree Grammar (RTG) which significantly expands the classes of structures that can be modelled. Our algorithm runs in O(n 6) time and the accuracy is reasonably high, with average PPV and sensitivity over 75%. In addition, the structures that RTG predicts are very similar to the real ones. |
Description | LNCS v. 9096 entitled: Bioinformatics Research and Applications: 11th International Symposium, ISBRA 2015 Norfolk, USA, June 7-10, 2015 Proceedings |
Persistent Identifier | http://hdl.handle.net/10722/219222 |
ISBN | |
ISSN | 2023 SCImago Journal Rankings: 0.606 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Li, M | - |
dc.contributor.author | Cheng, M | - |
dc.contributor.author | Ye, Y | - |
dc.contributor.author | Hon, WK | - |
dc.contributor.author | Ting, HF | - |
dc.contributor.author | Lam, TW | - |
dc.contributor.author | Tang, CY | - |
dc.contributor.author | Wong, T | - |
dc.contributor.author | Yiu, SM | - |
dc.date.accessioned | 2015-09-18T07:18:07Z | - |
dc.date.available | 2015-09-18T07:18:07Z | - |
dc.date.issued | 2015 | - |
dc.identifier.citation | The 11th International Symposium on Bioinformatics Research and Applications (ISBRA 2015), Norfolk, VA., 7-10 June 2015. In Lecture Notes in Computer Science, 2015, v. 9096, p. 211-222 | - |
dc.identifier.isbn | 978-3-319-19047-1 | - |
dc.identifier.issn | 0302-9743 | - |
dc.identifier.uri | http://hdl.handle.net/10722/219222 | - |
dc.description | LNCS v. 9096 entitled: Bioinformatics Research and Applications: 11th International Symposium, ISBRA 2015 Norfolk, USA, June 7-10, 2015 Proceedings | - |
dc.description.abstract | RNA secondary structures are known to be important in many biological processes. Many available programs have been developed for RNA secondary structure prediction. Based on our knowledge, however, there still exist secondary structures of known RNA sequences which cannot be covered by these algorithms. In this paper, we provide an efficient algorithm that can handle all RNA secondary structures found in Rfam database. We designed a new stochastic context-free grammar named Rectangle Tree Grammar (RTG) which significantly expands the classes of structures that can be modelled. Our algorithm runs in O(n 6) time and the accuracy is reasonably high, with average PPV and sensitivity over 75%. In addition, the structures that RTG predicts are very similar to the real ones. | - |
dc.language | eng | - |
dc.publisher | Springer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/ | - |
dc.relation.ispartof | Lecture Notes in Computer Science | - |
dc.rights | The final publication is available at Springer via http://dx.doi.org/[insert DOI] | - |
dc.title | Predicting RNA secondary structures: one-grammar-fits-all solution | - |
dc.type | Conference_Paper | - |
dc.identifier.email | Ting, HF: hfting@cs.hku.hk | - |
dc.identifier.email | Lam, TW: twlam@cs.hku.hk | - |
dc.identifier.email | Yiu, SM: smyiu@cs.hku.hk | - |
dc.identifier.authority | Ting, HF=rp00177 | - |
dc.identifier.authority | Lam, TW=rp00135 | - |
dc.identifier.authority | Yiu, SM=rp00207 | - |
dc.identifier.doi | 10.1007/978-3-319-19048-8_18 | - |
dc.identifier.scopus | eid_2-s2.0-84944527480 | - |
dc.identifier.hkuros | 252494 | - |
dc.identifier.volume | 9096 | - |
dc.identifier.spage | 211 | - |
dc.identifier.epage | 222 | - |
dc.identifier.isi | WOS:000362026100018 | - |
dc.publisher.place | Germany | - |
dc.customcontrol.immutable | sml 151014 | - |
dc.identifier.issnl | 0302-9743 | - |