Identifying bacterial genes and endosymbiont DNA with Glimmer

Abstract

Motivation: The Glimmer gene-finding software has been successfully used for finding genes in bacteria, archaea 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.

Fig. 1

Scoring an open reading frame from the stop codon backwards. The stop codon is at position 0 on the X-axis and the cumulative log-odds score is plotted as the solid line. Positions of possible start codons are indicated by vertical dashed lines. This ORF contains the fructose bis-P aldolase gene in Escherichia coli (EG14062) and the current Ecogene verified start site is at position 1050, near the peak score. This position is an update of the originally annotated start at position 1122.