Bioinformatics Software for Analyzing Microbial Genomes

用于分析微生物基因组的生物信息学软件

• 批准号: 8034822
• 负责人: Steven L. Salzberg
• 金额: $ 5.22万
• 依托单位: UNIV OF MARYLAND, COLLEGE PARK
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-03-25 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8034822
• 关键词: Address; Algorithms; Amino Acids; Anthrax disease; Archaea; Archaeal Genome; Bacteria; Bacterial Genome; Bioinformatics; Biological; Cholera; Code; Collection; Communities; Computer software; DNA; Data; Databases; Development; Disease; Eukaryota; Event; Genbank; Genes; Genetic Transcription; Genome; Genomics; Human Resources; Human body; Infection; Licensing; Life; Literature; Lyme Disease; Maintenance; Metagenomics; Nucleotides; Operon; Organism; Probability; Procedures; Proteins; Research; Research Personnel; Research Support; Running; Scientist; Source Code; Speed; Surveys; Syntenic Conservation; Syphilis; System; Time; Translations; Trees; Tuberculosis; Update; Viral Genome; Virus; Work; base; data structure; experience; genome sequencing; improved; insertion/deletion mutation; markov model; microbial genome; open source; rho; software development; software systems; tool; web site

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.

描述（由申请人提供）：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，所有这些系统都用于支持基因发现和基因组注释的研究。这些系统中最广泛使用的微光用于在细菌，病毒，古细菌和简单的真核生物中找到基因。在大多数细菌中，使用全自动程序发现了超过99％的基因。最近的文献调查表明，近年来，大多数细菌，病毒和古细菌基因组测序项目都使用了微光。该项目将通过几个新功能增强微光，包括扩展，以使闪光在元基因组学数据上使用。第二个系统，木乃伊是一个高效的全基因组对齐系统。近年来，Mummer已扩展了包装，使用户可以对齐基因组，使六框氨基酸翻译对齐，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软件，以启用多基因组对齐，并更自动地自动识别主要的基因组事件（反转和易位）。第三个系统，跨性别，发现细菌和古细菌基因组中的Rho非依赖性转录终结剂。 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，所有这些基因组都是可以自由下载的。该项目将扩展该软件以搜索抗终止剂，并允许其在不完整的基因组上运行，该基因组已经超过完成的基因组，并且正在继续迅速增长。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义识别核基因组中的操纵子。该项目将支持对软件的增强功能，并定期更新操作。该项目生成的所有软件和数据将继续在开源许可下免费提供，从而允许其他研究人员不受限制地使用新功能或将软件将软件连接到自己的系统中。该项目的项目叙述（相关性）支持一套软件包，这些软件包已广泛用于解释和分析许多致病生物，包括引起结核病，霍乱，炭疽，链球菌，链球菌，链球菌和staph感染，莱姆病，莱姆病，梅毒，梅毒和许多其他疾病的细菌。该软件的持续开发对于继续研究这些疾病将非常重要，并且在这里提出的新发展将是解决新的挑战，这些挑战将从努力序列序列序列的各种细菌序列。