NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments
Summary:Many natural nucleic acid sequences have evolutionarily conserved secondary structures with diverse biological functions. A reliable computational tool for identifying such structures would be very useful in guiding experimental analyses of their biological functions. NASP (Nucleic Acid Stru...
| Autores principales: | , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2011
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/68358 |
| _version_ | 1855521895604027392 |
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| author | Semegni, J.Y. Wamalwa, M. Gaujoux, R. Harkins, G.W. Gray, A.R. Martin, D. |
| author_browse | Gaujoux, R. Gray, A.R. Harkins, G.W. Martin, D. Semegni, J.Y. Wamalwa, M. |
| author_facet | Semegni, J.Y. Wamalwa, M. Gaujoux, R. Harkins, G.W. Gray, A.R. Martin, D. |
| author_sort | Semegni, J.Y. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Summary:Many natural nucleic acid sequences have evolutionarily conserved secondary structures with diverse biological functions. A reliable computational tool for identifying such structures would be very useful in guiding experimental analyses of their biological functions. NASP (Nucleic Acid Structure Predictor) is a program that takes into account thermodynamic stability, Boltzmann base pair probabilities, alignment uncertainty, covarying sites and evolutionary
conservation to identify biologically relevant secondary structures within multiple sequence alignments. Unique to NASP is the
consideration of all this information together with a recursive permutation-based approach to progressively identify and list the
most conserved probable secondary structures that are likely to have the greatest biological relevance. By focusing on identifying only evolutionarily conserved structures, NASP forgoes the prediction of
complete nucleotide folds but outperforms various other secondary structure prediction methods in its ability to selectively identify actual base pairings. |
| format | Journal Article |
| id | CGSpace68358 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2011 |
| publishDateRange | 2011 |
| publishDateSort | 2011 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace683582024-08-27T10:35:34Z NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments Semegni, J.Y. Wamalwa, M. Gaujoux, R. Harkins, G.W. Gray, A.R. Martin, D. nucleic acids Summary:Many natural nucleic acid sequences have evolutionarily conserved secondary structures with diverse biological functions. A reliable computational tool for identifying such structures would be very useful in guiding experimental analyses of their biological functions. NASP (Nucleic Acid Structure Predictor) is a program that takes into account thermodynamic stability, Boltzmann base pair probabilities, alignment uncertainty, covarying sites and evolutionary conservation to identify biologically relevant secondary structures within multiple sequence alignments. Unique to NASP is the consideration of all this information together with a recursive permutation-based approach to progressively identify and list the most conserved probable secondary structures that are likely to have the greatest biological relevance. By focusing on identifying only evolutionarily conserved structures, NASP forgoes the prediction of complete nucleotide folds but outperforms various other secondary structure prediction methods in its ability to selectively identify actual base pairings. 2011-09-01 2015-09-30T10:55:53Z 2015-09-30T10:55:53Z Journal Article https://hdl.handle.net/10568/68358 en Open Access Oxford University Press Semegni, J.Y., Wamalwa, M., Gaujoux, R., Harkins, G.W., Gray, A. and Martin, D.P. 2011. NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments. Bioinformatics 27(17):2443-2445. |
| spellingShingle | nucleic acids Semegni, J.Y. Wamalwa, M. Gaujoux, R. Harkins, G.W. Gray, A.R. Martin, D. NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments |
| title | NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments |
| title_full | NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments |
| title_fullStr | NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments |
| title_full_unstemmed | NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments |
| title_short | NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments |
| title_sort | nasp a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments |
| topic | nucleic acids |
| url | https://hdl.handle.net/10568/68358 |
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