AltAnalyze - An Optimized Platform for RNA-Seq Splicing and Domain-Level Analyses

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The deep sequencing of transcriptomes has revolutionized our ability to detect known and novel RNA variants at a never before observed resolution. To capitalize on these ever improving technologies, we require functionally rich methods of annotation to predict and evaluate the consequences of RNA isoform variation at the level of proteins, domains and microRNA binding sites. We introduce a new version of the popular open-source application AltAnalyze, capable of analyzing RNA-Sequencing (RNA-Seq) datasets as well as splicing-sensitive or conventional arrays. This software can be run through an intuitive graphical user interface or command-line. Over 60 species and data from various RNA-Seq alignment workflows are immediately supported without any specialized configuration. AltAnalyze provides multiple options for gene expression quantification, filtering, quality control and biological interpretation. Hierarchical clustering heatmaps, principal component analysis plots, lineage correlation diagrams and visualization of enriched pathways are automatically produced for differentially expressed genes. For detection of alternative splicing, promoter or polyadenylation events, AltAnalyze combines both reciprocal-junction and alternative-exon expression approaches to identify annotated and novel RNA variation. By connecting these regulated splicing-events with optimal inclusion and exclusion isoforms, AltAnalyze is able to evaluate the impact of alternative RNA expression on protein domains, annotated motifs and binding sites for microRNAs. From a broader perspective, AltAnalyze examines the enrichment of effected domains and microRNA binding sites, to highlight the global impact of alternative splicing. Together, AltAnalyze provides an efficient, streamlined and comprehensive set of analysis results, to determine the biological impact of transcriptome regulation.