Bioinformatics Software for Analyzing Microbial Genomes

项目描述（由申请人提供）：本项目将支持四个广泛用于基因发现和基因组注释研究的生物信息学软件系统的持续开发和维护。其中第一种，微光，被用来寻找细菌，病毒，古细菌和简单的真核生物的基因。Glimmer非常精确，在大多数细菌中发现了99%以上的基因。它已经被世界各地成千上万的科学家使用，包括在过去十年中发表的大多数细菌和档案基因组测序项目。描述Glimmer的三份主要出版物总共被引用了2600多次，其中仅2012年就被引用了400次。近年来，由于下一代测序项目的爆炸式增长，Glimmer的使用有所增加，这对细菌基因组来说尤其具有成本效益。我们最近推出了为met基因组学数据定制的新版本Glimmer，旨在使微生物组研究人员可以使用它。Glimmer的算法也是PhymmBL的基础，PhymmBL是一个用于从宏基因组项目中分类序列的新系统，我们也将在本项目下支持该系统。第二个系统，MUMmer，是一个高效的全基因组比对系统，广泛用于比较细菌基因组和比较基因组组装以检测大小变化。MUMmer及其组件，特别是Nucmer，已被广泛使用，并已纳入许多其他系统，包括最近的多基因组比对器，Mugsy和几个基因组组装包。描述MUMmer的三个主要出版物被引用超过1900次，其中2012年被引用200次。除了测序成本下降之外，最近这些系统使用量增加的一个主要原因是宏基因组学研究的增长，特别是人类微生物组项目。该项目还将支持另外两个系统，TransTermHP和OperonDB，以及与它们配套的web数据库。TransTermHP在细菌和古细菌基因组中发现转录终止子，我们已经用它建立了一个网站，其中包含超过1500个基因组的预测，所有这些都是免费下载的。OperonDB包括一个数据库和一个软件系统，该系统使用跨物种的保守合性识别原核基因组集合中的操纵子。这些系统中的每一个都被广泛使用和引用，这个项目需要资金来重建一个更大的基因组数据库，并随着更多基因组的出现而继续扩展它们。本项目生成的所有软件和数据将在开源许可下继续免费提供，允许其他研究人员不受任何限制地使用、修改和重新分发它们。

DESCRIPTION (provided by applicant): This project will support the continued development and maintenance of four bioinformatics software systems that are widely used in research on gene finding and genome annotation. The first of these, Glimmer, is used to find genes in bacteria, viruses, archaea, and simple eukaryotes. Glimmer is highly accurate, finding over 99% of the genes in most bacteria. It has been used by thousands of scientists around the world, including the majority of published bacterial and archival genome sequencing projects over the past decade. Collectively the three main publications describing Glimmer have been cited over 2,600 times, including 400 citations in 2012 alone. Usage of Glimmer has increased in recent years due to the explosion in next-generation sequencing projects, which are particularly cost-effective for bacterial genomes. Our very recent introduction of a new version of Glimmer customized for met genomics data is intended to make it available to microbiome researchers. Glimmer's algorithm is also the basis of PhymmBL, a new system for classifying sequences from metagenomics projects, which we will also support under this project. The second system, MUMmer, is a highly efficient system for whole-genome alignment that is widely used to compare bacterial genomes to one another and to compare genome assemblies to detect changes, both large and small. MUMmer and its components, especially Nucmer, have been widely used and have been incorporated in many other systems, including a recent multi-genome aligner, Mugsy, and several genome assembly packages. The three main publications describing MUMmer have been cited over 1,900 times including 200 citations in 2012. A major reason for the recent increase in usage of these systems, beyond the drop in sequencing costs, is the growth of metagenomics research, particularly the human microbiome project. This project will also support two other systems, TransTermHP and OperonDB, and the web databases that accompany them. TransTermHP finds transcription terminators in bacterial and archaeal genomes, and we have used it to build a website containing predictions for over 1500 genomes, all of which are freely downloadable. OperonDB includes a database and a software system that identifies operons in a collection of prokaryotic genomes using conserved synteny across species. Each of these systems have been widely used and cited, and this project requests funding to rebuild the databases on a larger collection of genomes and to continue to expand them as more genomes appear. All of the software and data generated by this project will continue to be freely available under an open source license, allowing unrestricted use by other researchers to use, modify, and redistribute them without restrictions of any kind.