Identifying bacterial genes and endosymbiont DNA with Glimmer

Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States
Bioinformatics (Impact Factor: 4.62). 04/2007; 23(6):673-9. DOI: 10.1093/bioinformatics/btm009
Source: PubMed

ABSTRACT 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.
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.
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    • "The overall accuracy of the finished sequence was estimated to have an error rate of <1 per 10,000 bases (Phrap score of ≥40). An initial set of predicted protein-coding genes was identified using Glimmer 3.0 (Delcher et al., 2007). Genes consisting of <120 base pairs (bp) and those containing overlaps were eliminated. "
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    • "The complete genome was achieved by filling the gaps between the junctions of contigs, using general PCR and Sanger sequencing method. Gene prediction was determined by using Glimmer 3.0 (Delcher et al., 2007). Genes coding tRNA and rRNA genes were determined through tRNAscan-SE and RNAmmer, respectively (Lowe and Eddy, 1997; Lagesen et al., 2007). "
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