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BMC Bioinformatics. 2012 May 8;13:84. doi: 10.1186/1471-2105-13-84.

Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny.

Author information

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

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). 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.

PMID:
22568790
PMCID:
PMC3424829
DOI:
10.1186/1471-2105-13-84
[Indexed for MEDLINE]
Free PMC Article

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