Identifying bacterial genes and endosymbiont DNA with Glimmer
Identifying bacterial genes and endosymbiont DNA with Glimmer
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DOI：
10.1093/bioinformatics/btm009
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发表时间：
2007-03-15
期刊：
影响因子：
5.8
通讯作者：
Salzberg, Steven L.
中科院分区：
文献类型：
--
作者：
Delcher, Arthur L.;Bratke, Kirsten A.;Salzberg, Steven L.
动机：Glimmer基因寻找软件已经成功地用于寻找细菌、真菌和病毒的基因，这些基因代表了数百种物种。我们描述了Glimmer系统的几个主要变化，包括识别编码区和起始密码子的改进方法。我们还描述了一个新的能够区分宿主和内共生DNA的Glimmer模块。该模块是针对真核生物基因组测序项目有时无意中捕获宿主细胞内细菌DNA的发现而开发的。结果：新方法大大降低了假阳性预测的比率，同时保持了Glimmer在大多数物种中检测基因的99%的灵敏度，并且通过与已知的和经过良好筛选的基因进行比较，他们发现了更正确的起始位点。我们表明，我们的插值马尔可夫模型（IMM） DNA鉴别器在最近的基因组计划中正确分离了99%的序列，该基因组计划产生了来自Prochloron didemni细菌和它的海鞘宿主Lissoclinum patella的序列混合物。
Motivation: The Glimmer gene-finding software has been successfully used for finding genes in bacteria, arch ae a 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 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.