PMID: 8972857Dec 1, 1996Paper

Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences

Nucleic Acids Research
J KleffeVolker Brendel

Abstract

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.

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Citations

Jul 9, 2004·Journal of Genetics·Akhilesh K TyagiSulabha Sharma
Jul 1, 1997·Journal of Molecular Evolution·I B Rogozin, L Milanesi
Jul 15, 1999·Computers & Chemistry·L VignalC Thermes
Mar 14, 2000·Current Opinion in Plant Biology·T Sasaki, B Burr
Oct 5, 2002·Nucleic Acids Research·Catherine MathéPierre Rouzé
Jan 10, 2003·Nucleic Acids Research·Delphine SamsonEmmanuel Barillot
Jul 11, 2006·Annual Review of Genomics and Human Genetics·Steven J M Jones
Apr 6, 2006·Biology Direct·Alexander ChurbanovHesham Ali
Dec 28, 1999·Proceedings of the National Academy of Sciences of the United States of America·S ChopraT Peterson
Apr 22, 2008·Plant Biotechnology Journal·Jost MuthDirk Prüfer
Oct 19, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jagath C Rajapakse, Loi Sy Ho
Mar 26, 1998·Journal of Molecular Biology·V BrendelV Walbot

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