Bioinformatics Software for Analyzing Microbial Genomes

项目描述（由申请人提供）：本项目将支持四个生物信息学软件系统的持续开发和维护，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Glimmer，用于发现细菌、病毒、古生菌和简单真核生物中的基因。Glimmer使用全自动程序发现大多数细菌中超过99%的基因。对最近文献的调查表明，近年来，Glimmer已被大多数细菌，病毒和古细菌基因组测序项目所使用。该项目将增强Glimmer的几个新功能，包括扩展，使Glimmer的使用宏基因组学数据。第二个系统MUMmer是一个高效的全基因组比对系统。近年来，MUMmer已经扩展了软件包，允许用户比对基因组草案，比对六框氨基酸翻译，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，发现细菌和古细菌基因组中的rho独立的转录终止子。TransTerm包括一个软件包和一个网站，其中包含数百个基因组的预测，所有这些都可以免费下载。该项目将扩展该软件，以搜索反终止子，并允许它对不完整的基因组进行操作，这些基因组的数量已经超过了完成的基因组，并将继续快速增长。第四个系统OperonDB包括一个数据库和一个软件系统，该系统使用跨物种的保守同线性来识别原核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，以添加新功能或将软件连接到自己的系统中。该项目支持一套软件包，这些软件包已被广泛用于解释和分析许多病原体，包括导致结核病、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。该软件的持续开发将对这些疾病的持续研究至关重要，这里提出的新发展将是必要的，以解决从对生活在人体中的各种细菌进行测序的努力中出现的新挑战。

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.