SpliceSeq: A Resource for Analysis and Visualization of RNA-Seq Data on Alternative Splicing and Its Functional Impacts.

SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing and identifies potential functional changes that result from splice variation. The application is a Java program that can be launched via a browser or installed locally. Local installation requires MySQL and Bowtie. It displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats.

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.

The 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 samples, or on groups of samples to identify statistically significant group level differences in splicing patterns. 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.

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