GenomeDiagram: a python package for the visualization of large-scale genomic data

Leighton Pritchard; Jennifer A White; Paul R J Birch; Ian K Toth

doi:10.1093/bioinformatics/btk021

GenomeDiagram: a python package for the visualization of large-scale genomic data

Bioinformatics. 2006 Mar 1;22(5):616-7. doi: 10.1093/bioinformatics/btk021. Epub 2005 Dec 23.

Authors

Leighton Pritchard¹, Jennifer A White, Paul R J Birch, Ian K Toth

Affiliation

¹ Plant Pathogen Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK. lpritc@scri.ac.uk

PMID: 16377612
DOI: 10.1093/bioinformatics/btk021

Abstract

We present GenomeDiagram, a flexible, open-source Python module for the visualization 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.

Publication types

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

MeSH terms

Chromosome Mapping / methods*
Computer Graphics*
Database Management Systems*
Databases, Genetic*
Information Storage and Retrieval / methods
Programming Languages*
Software*
User-Computer Interface*