Title | Pre-mRNA secondary structure prediction aids splice site prediction. |
Publication Type | Journal Article |
Year of Publication | 2002 |
Authors | Patterson DJ, Yasuhara K, Ruzzo WL |
Journal | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing |
Pagination | 223-34 |
Date or Month Published | 2002 |
ISSN | 1793-5091 |
Keywords | Computer Simulation, Exons, Likelihood Functions, Models, Genetic, Nucleic Acid Conformation, Reproducibility of Results, RNA, Messenger, RNA Precursors, RNA Splicing, Sequence Analysis, RNA, Software |
Abstract | Accurate 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. |
Downloads | http://www.ncbi.nlm.nih.gov/pubmed/11928478?dopt=Abstract |
Alternate Journal | Pac Symp Biocomput |
Citation Key | 1890 |
PubMed ID | 11928478 |