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A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana
BACKGROUND: Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites. RESULTS: We have devel...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2007
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892810/ https://www.ncbi.nlm.nih.gov/pubmed/17517127 http://dx.doi.org/10.1186/1471-2105-8-159 |
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author | Pertea, Mihaela Mount, Stephen M Salzberg, Steven L |
author_facet | Pertea, Mihaela Mount, Stephen M Salzberg, Steven L |
author_sort | Pertea, Mihaela |
collection | PubMed |
description | BACKGROUND: Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites. RESULTS: We have developed a new computational technique to identify significantly conserved motifs involved in splice site regulation. First, 84 putative exonic splicing enhancer hexamers are identified in Arabidopsis thaliana. Then a Gibbs sampling program called ELPH was used to locate conserved motifs represented by these hexamers in exonic regions near splice sites in confirmed genes. Oligomers containing 35 of these motifs have been shown experimentally to induce significant inclusion of A. thaliana exons. Second, integration of our regulatory motifs into two different splice site recognition programs significantly improved the ability of the software to correctly predict splice sites in a large database of confirmed genes. We have released GeneSplicerESE, the improved splice site recognition code, as open source software. CONCLUSION: Our results show that the use of the ESE motifs consistently improves splice site prediction accuracy. |
format | Text |
id | pubmed-1892810 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-18928102007-06-19 A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana Pertea, Mihaela Mount, Stephen M Salzberg, Steven L BMC Bioinformatics Research Article BACKGROUND: Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites. RESULTS: We have developed a new computational technique to identify significantly conserved motifs involved in splice site regulation. First, 84 putative exonic splicing enhancer hexamers are identified in Arabidopsis thaliana. Then a Gibbs sampling program called ELPH was used to locate conserved motifs represented by these hexamers in exonic regions near splice sites in confirmed genes. Oligomers containing 35 of these motifs have been shown experimentally to induce significant inclusion of A. thaliana exons. Second, integration of our regulatory motifs into two different splice site recognition programs significantly improved the ability of the software to correctly predict splice sites in a large database of confirmed genes. We have released GeneSplicerESE, the improved splice site recognition code, as open source software. CONCLUSION: Our results show that the use of the ESE motifs consistently improves splice site prediction accuracy. BioMed Central 2007-05-21 /pmc/articles/PMC1892810/ /pubmed/17517127 http://dx.doi.org/10.1186/1471-2105-8-159 Text en Copyright © 2007 Pertea et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Pertea, Mihaela Mount, Stephen M Salzberg, Steven L A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana |
title | A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana |
title_full | A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana |
title_fullStr | A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana |
title_full_unstemmed | A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana |
title_short | A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana |
title_sort | computational survey of candidate exonic splicing enhancer motifs in the model plant arabidopsis thaliana |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892810/ https://www.ncbi.nlm.nih.gov/pubmed/17517127 http://dx.doi.org/10.1186/1471-2105-8-159 |
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