AltAnalyze is a freely available, cross-platform application designed analyze conventional microarry data as well as assess changes in protein sequence, domain composition, and microRNA targeting from user RNA sequencing (RNASeq) or splicing sensitive microarrays (Affymetrix Exon, Gene and Junction arrays). To do this, AltAnalyze associates changes in exon or junction expression that lead to the alternative expression of associated mRNAs. Basic methods for conventional microarray analysis are also available (RMA summarization, statistics, annotation and pathway over-representation). RNASeq analyses are supported in version 2.0.

This software can be run from an inutitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph. To get answers to common questions, check out our mailing list or go to the AltAnalyze Support Site and Wiki.