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Bioinformatics Advance Access published online on July 17, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn361
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Sircah: A tool for the detection and visualisation of alternative transcripts

Eoghan D. Harrington 1 and Peer Bork 1,2,*

1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
2Max Delbrück Centre for Molecular Medicine, D-13092 Berlin, Germany.

*To whom correspondence should be addressed. Peer Bork, E-mail: bork{at}embl.de


  Abstract

Summary: Sircah is a flexible tool for the detection, analysis and visualisation 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 visualised in a variety of ways, allowing the creation of publication quality images.

Results:

Availability: 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.

Contact: bork{at}embl.de

Associate Editor: Dr. Trey Ideker

Received on February 22, 2008; revised on May 30, 2008; accepted on July 14, 2008

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