Identifying bacterial genes and endosymbiont DNA with Glimmer

Identifying bacterial genes and endosymbiont DNA with Glimmer

Vol. 23 no. 6 2007, pages 673-679 do:10.1093/bioinformatics/btm009 Received on August 3, 2006; revised on December 15, 2006; accepted on January 14, 2007 Advance Access publication January 19, 2007 | Arthur L. Delcher1,* , Kirsten A. Bratke2, Edwin C. Powers3 and Steven L. Salzberg1
The article discusses the improvements and new features of the Glimmer gene-finding software, which is widely used for identifying genes in bacteria, archaea, and viruses. The authors describe several enhancements to the Glimmer system, including improved methods for identifying coding regions and start codons, and a new module that can distinguish host and endosymbiont DNA. These improvements reduce false-positive predictions while maintaining high sensitivity in detecting genes. The new methods also improve the accuracy of start site predictions and integrate all gene predictions across an entire genome. The article also introduces a new use for the interpolated Markov model (IMM) to separate host and endosymbiont DNA in eukaryotic genome projects. The Glimmer 3.0 package is available as open-source software and has been tested on various datasets, showing significant improvements in accuracy and specificity compared to previous versions.The article discusses the improvements and new features of the Glimmer gene-finding software, which is widely used for identifying genes in bacteria, archaea, and viruses. The authors describe several enhancements to the Glimmer system, including improved methods for identifying coding regions and start codons, and a new module that can distinguish host and endosymbiont DNA. These improvements reduce false-positive predictions while maintaining high sensitivity in detecting genes. The new methods also improve the accuracy of start site predictions and integrate all gene predictions across an entire genome. The article also introduces a new use for the interpolated Markov model (IMM) to separate host and endosymbiont DNA in eukaryotic genome projects. The Glimmer 3.0 package is available as open-source software and has been tested on various datasets, showing significant improvements in accuracy and specificity compared to previous versions.
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