Abstract
Sircah is a flexible tool for the detection, analysis and visualization of alternative transcripts. It takes as input gene models or spliced alignments and creates a database of alternative transcription events: alternative transcription initiation and polyadenylation, alternative 3' and 5' splice-site usage, skipped exons and retained introns. The results can be visualized in a variety of ways, allowing the creation of publication quality images. The Sircah is available for download under a creative commons license along with additional documentation and a tutorial from http://www.bork.embl.de/Sircah.
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