Bioinformatics Software for Analyzing Microbial Genomes

项目描述（申请人提供）：该项目将支持四个生物信息学软件系统的持续开发和维护，这些软件系统广泛用于基因发现和基因组注释研究。第一个是Glimmer，用于发现细菌、病毒、古生菌和简单真核生物中的基因。Glimmer的准确率很高，可以找到大多数细菌中99%以上的基因。它已被世界各地成千上万的科学家使用，包括过去十年中大多数已发表的细菌和档案基因组测序项目。描述Glimmer的三个主要出版物被引用超过2，600次，其中仅2012年就有400次引用。近年来，由于下一代测序项目的爆炸式增长，Glimmer的使用量有所增加，这些项目对细菌基因组尤其具有成本效益。我们最近推出了针对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是一个新的系统，用于对宏基因组学项目中的序列进行分类，我们也将在该项目下提供支持。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，并已被纳入许多其他系统，包括最近的多基因组比对，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1，900次，其中2012年引用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，以及伴随它们的网络数据库。TransTermHP在细菌和古细菌基因组中发现了转录终止子，我们已经用它建立了一个网站，包含对1500多个基因组的预测，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同线性来识别原核基因组集合中的操纵子。这些系统都得到广泛使用和引用，本项目要求提供资金，以重建更大规模的基因组数据库，并随着更多基因组的出现继续扩大数据库。该项目生成的所有软件和数据将继续在开源许可证下免费提供，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.