A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons

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External Link(s)
https://doi.org/10.1186/1748-7188-1-14Date
2006-08-25Author
Allen, Jonathan E.
Salzburg, Steven S.
Citation
Allen, J.E., Salzberg, S.L. A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. Algorithms Mol Biol 1, 14 (2006).
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Show full item recordAbstract
Background: 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.
Results: 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 Drosophila melanogaster.
Conclusion: 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 Drosophila genomes to search for new cases of alternative
splicing.