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
Pagination223-34
Date or Month Published2002
ISSN1793-5091
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.
Downloadshttp://www.ncbi.nlm.nih.gov/pubmed/11928478?dopt=Abstract
Alternate JournalPac Symp Biocomput
Citation Key1890
PubMed ID11928478