A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
<p>Abstract</p> <p>Background</p> <p>An important challenge in eukaryotic gene prediction is accurate identification of alternatively spliced exons. Functional transcripts can go undetected in gene expression studies when alternative splicing only occurs under specific...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2006-08-01
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| Series: | Algorithms for Molecular Biology |
| Online Access: | http://www.almob.org/content/1/1/14 |
| _version_ | 1811297327333244928 |
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| author | Salzberg Steven L Allen Jonathan E |
| author_facet | Salzberg Steven L Allen Jonathan E |
| author_sort | Salzberg Steven L |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>An important challenge in eukaryotic gene prediction is accurate identification of alternatively spliced exons. Functional transcripts can go undetected in gene expression studies when alternative splicing only occurs under specific biological conditions. Non-expression based computational methods support identification of rarely expressed transcripts.</p> <p>Results</p> <p>A non-expression based statistical method is presented to annotate alternatively spliced exons using a single genome sequence and evidence from cross-species sequence conservation. The computational method is implemented in the program ExAlt and an analysis of prediction accuracy is given for <it>Drosophila melanogaster</it>.</p> <p>Conclusion</p> <p>ExAlt identifies the structure of most alternatively spliced exons in the test set and cross-species sequence conservation is shown to improve the precision of predictions. The software package is available to run on <it>Drosophila </it>genomes to search for new cases of alternative splicing.</p> |
| first_indexed | 2024-04-13T06:01:43Z |
| format | Article |
| id | doaj.art-a59ceed7b2e747cca7dbca4cf87eed62 |
| institution | Directory Open Access Journal |
| issn | 1748-7188 |
| language | English |
| last_indexed | 2024-04-13T06:01:43Z |
| publishDate | 2006-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Algorithms for Molecular Biology |
| spelling | doaj.art-a59ceed7b2e747cca7dbca4cf87eed622022-12-22T02:59:24ZengBMCAlgorithms for Molecular Biology1748-71882006-08-01111410.1186/1748-7188-1-14A phylogenetic generalized hidden Markov model for predicting alternatively spliced exonsSalzberg Steven LAllen Jonathan E<p>Abstract</p> <p>Background</p> <p>An important challenge in eukaryotic gene prediction is accurate identification of alternatively spliced exons. Functional transcripts can go undetected in gene expression studies when alternative splicing only occurs under specific biological conditions. Non-expression based computational methods support identification of rarely expressed transcripts.</p> <p>Results</p> <p>A non-expression based statistical method is presented to annotate alternatively spliced exons using a single genome sequence and evidence from cross-species sequence conservation. The computational method is implemented in the program ExAlt and an analysis of prediction accuracy is given for <it>Drosophila melanogaster</it>.</p> <p>Conclusion</p> <p>ExAlt identifies the structure of most alternatively spliced exons in the test set and cross-species sequence conservation is shown to improve the precision of predictions. The software package is available to run on <it>Drosophila </it>genomes to search for new cases of alternative splicing.</p>http://www.almob.org/content/1/1/14 |
| spellingShingle | Salzberg Steven L Allen Jonathan E A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons Algorithms for Molecular Biology |
| title | A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons |
| title_full | A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons |
| title_fullStr | A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons |
| title_full_unstemmed | A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons |
| title_short | A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons |
| title_sort | phylogenetic generalized hidden markov model for predicting alternatively spliced exons |
| url | http://www.almob.org/content/1/1/14 |
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