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Open Access Highly Accessed Software

OmniMapFree: A unified tool to visualise and explore sequenced genomes

John Antoniw12*, Andrew M Beacham1, Thomas K Baldwin1, Martin Urban1, Jason J Rudd1 and Kim E Hammond-Kosack1*

Author Affiliations

1 Centre for Sustainable Pest and Disease Management, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK

2 Centre for Mathematical and Computational Biology, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK

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BMC Bioinformatics 2011, 12:447  doi:10.1186/1471-2105-12-447

Published: 15 November 2011

Abstract

• Background

Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing volume of additional experimental information is available but this is rarely searchable within the landscape of the entire genome.

• Results

We have developed a generic software which permits users to view a single genome in entirety either within its chromosome or supercontig context within a single window. This software permits the genome to be displayed at any scales and with any features. Different data types and data sets are displayed onto the genome, which have been acquired from other types of studies including classical genetics, forward and reverse genetics, transcriptomics, proteomics and improved annotation from alternative sources. In each display, different types of information can be overlapped, then retrieved in the desired combinations and scales and used in follow up analyses. The displays generated are of publication quality.

• Conclusions

OmniMapFree provides a unified, versatile and easy-to-use software tool for studying a single genome in association with all the other datasets and data types available for the organism.