2/21/2014 - A patch release, SpliceSeq 2.1 has been released. The patch includes minor bug fixes, and update of the SpliceGraph database and turns off a component in group / group comparison analysis that was causing excessively long loads.
|Description||A tool for investigating alternative mRNA splicing in next generation mRNA sequence data|
|License||Freely available for academic and commercial use.|
|Last Updated||February 21, 2014|
|Citations||Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN(2012). SpliceSeq: A Resource for Analysis and Visualization of RNA-Seq Data on Alternative Splicing and Its Functional Impacts. Bioinformatics, 10.1093.|
|Help and Support|
|Discussion||Discussion on Github|
SpliceViewer is a Java application that allows researchers to investigate alternative mRNA splicing patterns in data from high-throughput mRNA sequencing studies. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing.
This tool may be used on a single RNASeq sample to identify genes with multiple spliceforms, on a pair of samples to identify differential splicing between the two, or on groups of samples to identify statistically significant group level differences in splicing patterns.
SpliceSeq can be run from the install page as a java web start application to explore the sequencing data on our server or can be installed locally to analyze your own mRNA-Seq data.
Several YouTube tutorials have been developed for SpliceSeq. Please maximize and switch to 1080p resolution for best viewing.
Here you can find basic help on installation, usage and methodology.