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AltAnalyze is a freely available, open-source and cross-platform program that allows you to take RNASeq or relatively raw microarray data (CEL files or normalized), identify predicted alternative splicing or alternative promoter changes and view how these changes may affect protein sequence, domain composition, and microRNA targeting.

AltAnalyze is compatible with any RNASeq data that can be aligned to junctions, several Affymetrix splicing sensitive array types (Gene 1.0, Exon 1.0, junction) as well as many conventional array-types (e.g., Affymetrix, Illumina, Agilent). This software requires no advanced knowledge of bioinformatics programs or scripting. All you will need are your junction read or microarray files along with some simple descriptions of the conditions that you're analyzing. RNASeq support is introduced in AltAnalyze 2.0.