Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
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DOI：
10.1093/bioinformatics/bti015
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发表时间：
2005-02-01
期刊：
影响因子：
5.8
通讯作者：
White, O
中科院分区：
文献类型：
--
作者：
Haft, DH;Selengut, JD;White, O
动机：代谢途径和结构的存在或不存在提供了使蛋白质注释更加可靠的背景。编译这些信息在微生物基因组提高了蛋白质的功能分类，并提供了一个宝贵的资源比较genomics.Results：我们已经创建了一个基因组属性系统，目前使用标准化的计算方法和控制词汇的原核生物学的关键方面。属性反映了基因内容、表型、遗传和计算分析。使用隐马尔可夫模型的搜索结果允许自动推导出许多属性，特别是对于自其最后共同祖先以来功能保守的蛋白质家族（等价物）。其他属性来自策展，发表的报告和其他形式的证据。基因组属性系统应用于156个完整的原核生物基因组，并且很容易挖掘到物种之间的差异，代谢特征和未表征蛋白质家族之间的相关性，或属性之间的关系。
Motivation: The presence or absence of metabolic pathways and structures provide a context that makes protein annotation far more reliable. Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics.Results: We have created a Genome Properties system to present key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties.