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Identifying bacterial genes and endosymbiont DNA with Glimmer

dc.contributor.authorDelcher, Arthur L.
dc.contributor.authorBratke, Kirsten A.
dc.contributor.authorPowers, Edwin C.
dc.contributor.authorSalzberg, Steven L.
dc.identifier.citationIdentifying bacterial genes and endosymbiont DNA with Glimmer. A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Bioinformatics 2007 Mar 15;23(6):673-9.en
dc.description.abstractMotivation: The Glimmer gene-finding software has been successfully used for finding genes in bacteria, archæa 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 falsepositive 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.en
dc.format.extent141309 bytes
dc.subjectgene-finding softwareen
dc.subjectcoding regionsen
dc.subjectstart codonsen
dc.subjectendosymbiont DNAen
dc.subjecthost DNAen
dc.subjectMarkov model (IMM)en
dc.subjectProchloron didemnien
dc.subjectLissoclinum patellaen
dc.titleIdentifying bacterial genes and endosymbiont DNA with Glimmeren
dc.relation.isAvailableAtCollege of Computer, Mathematical & Physical Sciencesen_us
dc.relation.isAvailableAtComputer Scienceen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us

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