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URL: http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview
Proper Citation: SpliceSeq (RRID:SCR_005267)
Description: A Java application 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 their server or can be installed locally to analyze your own mRNA-Seq data.
Abbreviations: SpliceSeq
Resource Type: data analysis software, data processing software, software application, software resource
Keywords: rna-seq, mrna splicing pattern
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