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Open Access Software

Integrated functional visualization of eukaryotic genomes

Rohit Ghai*, Hannes Lindemann and Trinad Chakraborty

Author Affiliations

Institute of Medical Microbiology, Faculty of Medicine, Justus-Liebig University, Frankfurter Strasse 107, 35392 – Giessen, Germany

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BMC Bioinformatics 2006, 7:348  doi:10.1186/1471-2105-7-348

Published: 18 July 2006

Abstract

Background

Increasing amounts of data from large scale whole genome analysis efforts demands convenient tools for manipulation, visualization and investigation. Whole genome plots offer an intuitive window to the analysis. We describe two applications that enable users to easily plot and explore whole genome data from their own or other researchers' experiments.

Results

STRIPE and GFFtool (General Feature Format Tool) are softwares designed to support integration, visualization and exploration of whole genome data from eukaryotic genomes. STRIPE, in addition to providing a highly customizable and interactive data plot, provides access to numerous well-selected databases with updated information on all genes of a genome. GFFtool provides a user-friendly solution to integrating experimental data with the genomic information available in public databases. They also obviate the need for users to maintain large annotation resources, as they link to well-known resources using standard gene and protein identifiers.

Conclusion

The programs provide the user with broad genomic overviews of data distribution, fast access to data of interest, and the ability to navigate speedily from one resource to another, and gain a better understanding of result of whole genome analysis experiments.