Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences
| Autor: | Volker Brendel, Jürgen Kleffe, Klaus Hermann, Wolfgang Vahrson, Burkhardt Wittig |
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| Rok vydání: | 1996 |
| Předmět: |
Genetics
Splice site mutation RNA Splicing Molecular Sequence Data Arabidopsis Intron food and beverages Exons Computational biology Biology Zea mays Introns Exon RNA Plant RNA splicing Linear Models RNA Precursors splice RNA Messenger Precursor mRNA Gene Algorithms Research Article Sequence (medicine) |
| Zdroj: | Nucleic Acids Research. 24:4709-4718 |
| ISSN: | 1362-4962 |
| DOI: | 10.1093/nar/24.23.4709 |
| Popis: | Pre-mRNA splicing in plants, while generally similar to the processes in vertebrates and yeast, is thought to involve plant specific cis-acting elements. Both monocot and dicot introns are typically strongly enriched in U nucleotides, and AU- or U-rich segments are thought to be involved in intron recognition, splice site selection, and splicing efficiency. We have applied logitlinear models to find optimal combinations of splice site variables for the purpose of separating true splice sites from a large excess of potential sites. It is shown that plant splice site prediction from sequence inspection is greatly improved when compositional contrast between exons and introns is considered in addition to degree of matching to the splice site consensus (signal quality). The best model involves subclassification of splice sites according to the identity of the base immediately upstream of the GU and AG signals and gives substantial performance gains compared with conventional profile methods. |
| Databáze: | OpenAIRE |
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