Features generated for computational splice-site prediction correspond to functional elements

dc.contributor.authorDogan, Rezarta Islamaj
dc.contributor.authorGetoor, Lise
dc.contributor.authorWilbur, W John
dc.contributor.authorMount, Stephen M
dc.date.accessioned2021-12-06T19:18:49Z
dc.date.available2021-12-06T19:18:49Z
dc.date.issued2007-10-24
dc.description.abstractAccurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and introns. We previously described a feature generation algorithm (FGA) that is capable of achieving high classification accuracy on human 3' splice sites. In this paper, we extend the splice-site prediction to 5' splice sites and explore the generated features for biologically meaningful splicing signals. We present examples from the observed features that correspond to known signals, both core signals (including the branch site and pyrimidine tract) and auxiliary signals (including GGG triplets and exon splicing enhancers). We present evidence that features identified by FGA include splicing signals not found by other methods. Our generated features capture known biological signals in the expected sequence interval flanking splice sites. The method can be easily applied to other species and to similar classification problems, such as tissue-specific regulatory elements, polyadenylation sites, promoters, etc.en_US
dc.description.urihttps://doi.org/10.1186/1471-2105-8-410
dc.identifierhttps://doi.org/10.13016/eniw-mmwx
dc.identifier.citationDogan, R.I., Getoor, L., Wilbur, W.J. et al. Features generated for computational splice-site prediction correspond to functional elements. BMC Bioinformatics 8, 410 (2007).en_US
dc.identifier.urihttp://hdl.handle.net/1903/28202
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Natural 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
dc.subjectSplice Siteen_US
dc.subjectComposite Featureen_US
dc.subjectExonic Splice Enhanceren_US
dc.subjectBranch Siteen_US
dc.subjectTrue Splice Siteen_US
dc.titleFeatures generated for computational splice-site prediction correspond to functional elementsen_US
dc.typeArticleen_US

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