Bioinformatics Software for Analyzing Microbial Genomes

描述(申请人提供)：该项目将支持继续开发和维护四个生物信息学软件系统，所有这些软件系统都用于支持基因发现和基因组注释的研究。这些系统中使用最广泛的是GIMMER，用于在细菌、病毒、古菌和简单的真核生物中寻找基因。Glimmer使用全自动程序在大多数细菌中发现了99%以上的基因。一项对最近文献的调查表明，近年来大多数细菌、病毒和古生菌基因组测序项目都使用了GIMMER。该项目将通过几个新功能来增强Gimmer，包括扩展以使Gimmer能够在元基因组数据上使用。第二个系统，Mummer，是一种用于全基因组比对的高效系统。近年来，Mummer已经扩展了程序包，允许用户比对草稿基因组，比对六个框架的氨基酸翻译，并找到两个基因组之间的所有单核苷酸变化。该项目将进一步维护和扩展该软件，以实现多基因组比对，并更自动地识别主要基因组事件(倒位和易位)。第三个系统，TransTerm，在细菌和古菌基因组中找到Rho不依赖的转录终止子。TransTerm由一个软件包和一个网站组成，其中包含对数百个基因组的预测，所有这些都可以免费下载。这个项目将扩展软件以搜索反终止子，并允许它对不完整的基因组进行操作，这些不完整的基因组已经超过了完成的基因组，并且还在继续快速增长。第四个系统，OperonDB，包括一个数据库和一个软件系统，该系统使用保守的跨物种同时性识别原核生物基因组集合中的操纵子。该项目将支持对软件的增强和对OperonDB的定期更新。该项目产生的所有软件和数据将继续在开放源码许可下免费提供，允许其他研究人员不受限制地使用，以添加新功能或将软件连接到他们自己的系统中。项目简介(相关性)本项目支持一套广泛用于解释和分析许多病原体的软件包，包括引起结核病、霍乱、炭疽、链球菌和葡萄球菌感染、莱姆病、梅毒和许多其他疾病的细菌。正在进行的这一软件的开发对继续研究这些疾病将是至关重要的，这里提出的新开发将是必要的，以应对因对生活在人体内的各种细菌进行排序而出现的新挑战。

DESCRIPTION (provided by applicant): This project will support the continued development and maintenance of four bioinformatics software systems, all of which are used to support research on gene finding and genome annotation. The most widely used of these systems, Glimmer, is used to find genes in bacteria, viruses, archaea, and simple eukaryotes. Glimmer finds over 99% of the genes in most bacteria using a fully automated procedure. A survey of recent literature indicates that Glimmer has been used by the majority of bacterial, viral, and archaeal genome sequencing projects in recent years. This project will enhance Glimmer with several new features, including extensions to enable Glimmer's use on metagenomics data. The second system, MUMmer, is a highly efficient system for whole-genome alignment. In recent years MUMmer has been extended with packages that allow the user to align draft genomes, to align six-frame amino acid translations, and to find all single nucleotide changes between two genomes. This project will maintain and extend the software further, to enable multi-genome alignment and to identify major genomic events (inversions and translocations) more automatically. The third system, TransTerm, finds rho-independent transcription terminators in bacterial and archaeal genomes. TransTerm comprises a software package and a website containing predictions for hundreds of genomes, all of which are freely downloadable. This project will extend the software to search for anti-terminators, and to allow it to operate on incomplete genomes, which already outnumber finished genomes and are continuing to grow rapidly. The fourth system, OperonDB, includes a database and a software system that identifies operons in a collection of prokaryotic genomes using conserved synteny across species. This project will support enhancements to the software and regular updates to OperonDB. All of the software and data generated by this project will continue to be made available for free under an open source license, allowing unrestricted use by other researchers to add new functions or to wire the software into their own systems. Project Narrative (Relevance) This project supports a suite of software packages that have been extensively used in the interpretation and analysis of many pathogenic organisms, including the bacteria that cause tuberculosis, cholera, anthrax, strep and staph infections, Lyme disease, syphilis, and many other diseases. Ongoing development of this software will be of fundamental important in continuing research on these diseases, and new developments proposed here will be necessary to address the new challenges that will emerge from efforts to sequence the diverse bacteria that live in the human body.