Identifying bacterial genes and endosymbiont DNA with Glimmer

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…

• NS
  National Science Foundation

  Award: 0412226
• NI
  National Institutes of Health

  Awards: R01-LM006845, W81XWH
• NI
  National Institute of Allergy and Infectious Diseases
• DO
  Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases