对耶尔森氏菌的蛋白质基因组学更新：增强基因组注释。
A proteogenomic update to Yersinia: enhancing genome annotation.
机构信息
J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
出版信息
BMC Genomics. 2010 Aug 5;11:460. doi: 10.1186/1471-2164-11-460.
BACKGROUND
Modern biomedical research depends on a complete and accurate proteome. With the widespread adoption of new sequencing technologies, genome sequences are generated at a near exponential rate, diminishing the time and effort that can be invested in genome annotation. The resulting gene set contains numerous errors in even the most basic form of annotation: the primary structure of the proteins.
RESULTS
The application of experimental proteomics data to genome annotation, called proteogenomics, can quickly and efficiently discover misannotations, yielding a more accurate and complete genome annotation. We present a comprehensive proteogenomic analysis of the plague bacterium, Yersinia pestis KIM. We discover non-annotated genes, correct protein boundaries, remove spuriously annotated ORFs, and make major advances towards accurate identification of signal peptides. Finally, we apply our data to 21 other Yersinia genomes, correcting and enhancing their annotations.
CONCLUSIONS
In total, 141 gene models were altered and have been updated in RefSeq and Genbank, which can be accessed seamlessly through any NCBI tool (e.g. blast) or downloaded directly. Along with the improved gene models we discover new, more accurate means of identifying signal peptides in proteomics data.
背景
现代生物医学研究依赖于完整而准确的蛋白质组。随着新测序技术的广泛采用，基因组序列的生成速度呈近指数级增长，用于基因组注释的时间和精力也随之减少。即使是最基本形式的注释（蛋白质的一级结构），在基因集中也包含了许多错误。
结果
将实验蛋白质组学数据应用于基因组注释，称为蛋白质基因组学，可以快速有效地发现错误注释，从而产生更准确和完整的基因组注释。我们对鼠疫菌（Yersinia pestis KIM）进行了全面的蛋白质基因组分析。我们发现了未注释的基因，纠正了蛋白质边界，去除了错误注释的 ORF，并在准确识别信号肽方面取得了重大进展。最后，我们将我们的数据应用于 21 个其他的耶尔森氏菌基因组，纠正和增强了它们的注释。
结论
总共改变了 141 个基因模型，并已在 RefSeq 和 Genbank 中更新，可通过任何 NCBI 工具（例如 blast）无缝访问，或直接下载。除了改进的基因模型外，我们还发现了新的、更准确的方法来识别蛋白质组学数据中的信号肽。
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