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Nucleic Acids Research Advance Access published online on June 6, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm377
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case

G.X. Yu1,2, E.E. Snyder1, S.M. Boyle3, O.R. Crasta1, M. Czar1, S.P. Mane1, A. Purkayastha1, B. Sobral1 and J.C. Setubal1,*

1Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, 2Department of Biology and Department of Computer Science, Boise State University, Boise, ID 83726 and 3Center for Molecular Medicine and Infectious Diseases, Virginia–Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA

*To whom correspondence should be addressed. Tel: +1 540 231 9464; Fax: +1 540 231 2606; Email: setubal{at}vbi.vt.edu

Received January 22, 2007. Revised April 20, 2007. Accepted April 30, 2007.

We present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence variants such as genes with disrupted reading frames (split genes) and those with insertions and deletions (indels). For a given genome to be analyzed, GenVar relies on a database containing closely related genomes (such as other species or strains) as well as a few additional reference genomes. GenVar also helps identify gene disruptions probably caused by sequencing errors. We exemplify GenVar's capabilities by presenting results from the analysis of four Brucella genomes. Brucella is an important human pathogen and zoonotic agent. The analysis revealed hundreds of missed gene calls, new split genes and indels, several of which are species specific and hence provide valuable clues to the understanding of the genome basis of Brucella pathogenicity and host specificity.


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