Jan 24, 2007

Identifying bacterial genes and endosymbiont DNA with Glimmer

Bioinformatics
Arthur L DelcherSteven L Salzberg

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.

  • References23
  • Citations1324

References

Mentioned in this Paper

Mutualism
Protoplasm
Archaea
Morphologic Artifacts
Genome Mapping
Computer Programs and Programming
Codon, Initiator
Genes, Bacterial
Sequence Determinations, DNA
Illex

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.