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Bioinformatics Advance Access published online on January 19, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm009
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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.

Identifying bacterial genes and endosymbiont DNA with Glimmer

Arthur L. Delcher 1,*, Kirsten A. Bratke 2, Edwin C. Powers 3 and Steven L. Salzberg 1

1Center for Bioinformatics & Computational Biology, University of Maryland, College Park, MD 20742
2Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Ireland
3Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218

*To whom correspondence should be addressed. Arthur L. Delcher, E-mail: adelcher{at}umiacs.umd.edu


  Abstract

Motivation: The Glimmer gene-finding software has been successfully used for finding genes in bacteria, archæa, and viruses representing hundreds of species. We describe several major changes to the Glimmer system, including improved methods for identifying both coding regions and start codons. We also describe a new module of Glimmer that can distinguish host and endosymbiont DNA. This module was developed in response to the discovery that eukaryotic genome sequencing projects sometimes inadvertently capture the DNA of intracellular bacteria living in the host.

Results: The new methods dramatically reduce the rate of false-positive predictions, while maintaining Glimmer’s 99% sensitivity rate at detecting genes in most species, and they find substantially more correct start sites, as measured by comparisons to known and well-curated genes. We show that our interpolated Markov model (IMM) DNA discriminator correctly separated 99% of the sequences in a recent genome project that produced a mixture of sequences from the bacterium Prochloron didemni and its sea squirt host, Lissoclinum patella.

Availability: Glimmer is OSI Certified Open Source and available at http://cbcb.umd.edu/software/glimmer

Associate Editor: Alfonso Valencia

Received on August 3, 2006; revised on December 15, 2006; accepted on January 14, 2007

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