Article

Identifying bacterial genes and endosymbiont DNA with GLIMMER

Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States
Bioinformatics (Impact Factor: 4.98). 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.
Glimmer is OSI Certified Open Source and available at http://cbcb.umd.edu/software/glimmer.

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Available from: ncbi.nlm.nih.gov
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    • "The complete ACN001 genome sequence was analysed using Glimmer 3.0[10,11]and GeneMark[12,13]for gene prediction, the tRNAscan-SE tool for tRNA identi- fication[14], and RNAmmer[15]for ribosomal RNA identification. The predicted protein-coding genes were translated into amino acid sequences and annotated using the NCBI and UniProt non-redundant sequence databases[16], the Kyoto Encyclopedia of Genes and Genomes database[17], and, subsequently, the Cluster of Orthologous Genes database[18]to identify the specific protein products and their functional categories. "
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    • "Predicted genes were identified using Glimmer version 3.0[14]. tRNAscan-SE version 1.21[15]was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer version 1.2[16]. "
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    • "The high-quality reads, which provided an approximately 285-fold depth of coverage were assembled with Velvet Version 1.2.10 [5]. Protein-coding sequences were predicted by Glimmer software version 3.0 [6], while Ribosomal RNA (rRNA) and transfer RNA (tRNA) genes were predicted using an RNAmmer 1.2 server [7] and tRNAscan-SE Search Server version 1.21 [8] , respectively. Tandem repeats were predicted using Tandem Repeats Finder Version 4.04. "
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