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A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons

dc.contributor.authorAllen, Jonathan E.
dc.contributor.authorSalzburg, Steven S.
dc.date.accessioned2008-06-10T18:59:21Z
dc.date.available2008-06-10T18:59:21Z
dc.date.issued2006-08-25
dc.identifier.citationA phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. J.E. Allen and S.L. Salzberg. Algorithms for Molecular Biology 1:14 (2006).en
dc.identifier.urihttp://hdl.handle.net/1903/7997
dc.description.abstractBackground: 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.en
dc.format.extent723469 bytes
dc.format.mimetypeapplication/pdf
dc.language.isoen_USen
dc.publisherAlgorithms for Molecular Biologyen
dc.subjecteukaryotic gene predictionen
dc.subjectalternatively spliced exonsen
dc.subjectgene expressionen
dc.subjectExAlten
dc.titleA phylogenetic generalized hidden Markov model for predicting alternatively spliced exonsen
dc.typeArticleen
dc.relation.isAvailableAtCollege of Computer, Mathematical & Physical Sciencesen_us
dc.relation.isAvailableAtComputer Scienceen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us


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