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Open Access Software

Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny

Douglas B Craig1, Sujatha Kannan12 and Alan A Dombkowski1*

Author Affiliations

1 Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA

2 Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, USA

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BMC Bioinformatics 2012, 13:84  doi:10.1186/1471-2105-13-84

Published: 8 May 2012

Abstract

Background

The rabbit is an important model organism used in a wide range of biomedical research. However, the rabbit genome is still sparsely annotated, thus prohibiting extensive functional analysis of gene sets derived from whole-genome experiments. We developed a web-based application that provides augmented annotation and orthologue analysis for rabbit genes. Importantly, the application allows comprehensive functional analysis through the use of orthologous relationships.

Results

Using data extracted from several public bioinformatics repositories we created Better Bunny, a database and query tool that extensively augments the available functional annotation for rabbit genes. Using the complete set of target genes from a commercial rabbit gene expression microarray as our benchmark, we are able to obtain functional information for 88 % of the genes on the microarray. Previously, functional information was available for fewer than 10 % of the rabbit genes.

Conclusions

We have developed a freely available, web-accessible bioinformatics tool that enables investigators to quickly and easily perform extensive functional analysis of rabbit genes (http://cptweb.cpt.wayne.edu webcite). The software application fills a critical void for a wide range of biomedical research that relies on the rabbit model and requires characterization of biological function for large sets of genes.

Keywords:
Rabbit; Genome; Annotation; Orthologue; Microarray; Functional analysis