Identifying bacterial genes and endosymbiont DNA with Glimmer
Identifying bacterial genes and endosymbiont DNA with Glimmer
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Date
2007-03
Authors
Delcher, Arthur L.
Bratke, Kirsten A.
Powers, Edwin C.
Salzberg, Steven L.
Advisor
Citation
Identifying bacterial genes and endosymbiont DNA with Glimmer. A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Bioinformatics 2007 Mar 15;23(6):673-9.
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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 falsepositive
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.