Bioinformatics Software for Analyzing Microbial Genomes

描述(申请人提供)：该项目将支持四个生物信息学软件系统的继续开发和维护，这些软件系统广泛用于基因发现和基因组注释的研究。第一个是GIMMER，用于在细菌、病毒、古菌和简单的真核生物中寻找基因。Gimmer非常准确，在大多数细菌中找到了99%以上的基因。它已经被世界各地的数千名科学家使用，包括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Gimmer的三种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性增长，Gimmer的使用有所增加，这对细菌基因组来说尤其具有成本效益。我们最近推出了一种为MET基因组数据定制的新版本的Gimmer，目的是让微生物组研究人员能够使用它。Glimmer的算法也是Phymm BL的基础，这是一个用于从元基因组学项目中对序列进行分类的新系统，我们也将在该项目下支持该系统。第二个系统Mummer是一种高效的全基因组比对系统，广泛用于比较细菌基因组之间的差异，并比较基因组组合以检测大小的变化。Mummer及其组件，特别是Nucmer，已经被广泛使用并被整合到许多其他系统中，包括最近的多基因组比对程序Mugsy和几个基因组组装包。描述木乃伊的三种主要出版物被引用超过1900次，其中2012年被引用了200次。除了测序成本的下降外，最近这些系统的使用增加的一个主要原因是元基因组研究的增长，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，以及伴随它们的网络数据库。TransTermHP在细菌和古生菌基因组中发现了转录终止子，我们利用它建立了一个网站，其中包含对1500多个基因组的预测，所有这些都可以免费下载。OperonDB包括一个数据库和一个软件系统，它使用保守的跨物种同步性来识别原核生物基因组集合中的操纵子。这些系统中的每一个都得到了广泛的使用和引用，该项目要求提供资金，以重建更大的基因组集合上的数据库，并随着更多基因组的出现而继续扩大数据库。该项目生成的所有软件和数据将继续在开放源码许可证下免费使用，允许其他研究人员不受限制地使用、修改和重新分发它们，而不受任何类型的限制。

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.