TitlePre-mRNA secondary structure prediction aids splice site prediction.
Publication TypeJournal Article
Year of Publication2002
AuthorsPatterson DJ, Yasuhara K, Ruzzo WL
JournalPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Date or Month Published2002
KeywordsComputer Simulation, Exons, Likelihood Functions, Models, Genetic, Nucleic Acid Conformation, Reproducibility of Results, RNA, Messenger, RNA Precursors, RNA Splicing, Sequence Analysis, RNA, Software
AbstractAccurate splice site prediction is a critical component of any computational approach to gene prediction in higher organisms. Existing approaches generally use sequence-based models that capture local dependencies among nucleotides in a small window around the splice site. We present evidence that computationally predicted secondary structure of moderate length pre-mRNA subsequencies contains information that can be exploited to improve acceptor splice site prediction beyond that possible with conventional sequence-based approaches. Both decision tree and support vector machine classifiers, using folding energy and structure metrics characterizing helix formation near the splice site, achieve a 5-10% reduction in error rate with a human data set. Based on our data, we hypothesize that acceptors preferentially exhibit short helices at the splice site.
Alternate JournalPac Symp Biocomput
Citation Key1890
PubMed ID11928478