Sircah: a tool for the detection and visualization of alternative transcripts

Eoghan D Harrington; Peer Bork

doi:10.1093/bioinformatics/btn361

Sircah: a tool for the detection and visualization of alternative transcripts

Bioinformatics. 2008 Sep 1;24(17):1959-60. doi: 10.1093/bioinformatics/btn361. Epub 2008 Jul 17.

Authors

Eoghan D Harrington¹, Peer Bork

Affiliation

¹ Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

PMID: 18635569
DOI: 10.1093/bioinformatics/btn361

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.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Base Sequence
Computer Graphics*
Molecular Sequence Data
RNA Splice Sites / genetics*
Sequence Analysis, DNA / methods*
Software*
Transcription Factors / genetics*
User-Computer Interface*

Substances

RNA Splice Sites
Transcription Factors