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Bioinformatics Advance Access published online on December 23, 2005
Bioinformatics, doi:10.1093/bioinformatics/btk021
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received October 27, 2005
Revised December 8, 2005
Accepted December 21, 2005

Applications note

GenomeDiagram: a Python package for the visualisation of large-scale genomic data

Leighton Pritchard 1 *, Jennifer A. White 1, Paul R. J. Birch 1, and Ian K. Toth 1

1 Plant Pathogen Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, Scotland UK

* To whom correspondence should be addressed.
Leighton Pritchard, E-mail: lpritc{at}scri.ac.uk


  Abstract

Summary: We present GenomeDiagram, a flexible, open-source Python module for the visualisation of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images, and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems.

Availability: GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages.

Supplementary Information: A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.


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