SplicePort--an interactive splice-site analysis tool.
SplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we have found capable of providing high classification accuracy on human splice sites. Feature selection is optimized for human splice sites, but the selected features are likely to be predictive for other mammals as well. With our interactive feature browsing and visualization tool, the user can view and explore subsets of features used in splice-site prediction (either the features that account for the classification of a specific input sequence or the complete collection of features). Selected feature sets can be searched, ranked or displayed easily. The user can group features into clusters and frequency plot WebLogos can be generated for each cluster. The user can browse the identified clusters and their contributing elements, looking for new interesting signals, or can validate previously observed signals. The SplicePort web server can be accessed at http://www.cs.umd.edu/projects/SplicePort and http://www.spliceport.org.
Dogan
Rezarta Islamaj
RI
Computer Science Department, University of Maryland, College Park, Maryland 20742, USA. rezarta@cs.umd.edu
Getoor
Lise
L
Wilbur
W John
WJ
Mount
Stephen M
SM
D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000235:genetics*; D016678:Genome; D006801:Humans; D020407:Internet; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D022821:RNA Splice Sites / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D014584:User-Computer Interface
D022821:RNA Splice Sites; D004247:DNA