GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes
GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes
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GAPP：用于原核生物基因组注释和翻译后修饰全局分析的蛋白质基因组软件
DOI：
10.1074/mcp.m116.060046
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发表时间：
2016
影响因子：
7
通讯作者：
Ge Feng
中科院分区：
文献类型：
--
作者：
Zhang Jia;Yang Ming-kun;Zeng Honghui;Ge Feng
虽然原核生物基因组测序的数量正在迅速增长，但实验验证的原核生物基因组注释仍然不完整且具有挑战性。为了促进原核生物的基因组注释工作，我们开发了一个名为GAPP的开源软件，用于原核生物的基因组注释和翻译后修饰（PTM）的全局分析。通过一个命令，它提供了一个标准的工作流程来验证和优化预测的遗传模型，并发现不同的PTM事件。我们使用幽门螺杆菌的蛋白质组数据证明了GAPP的实用性，幽门螺杆菌是导致许多胃部疾病的主要人类病原体之一。我们的结果证实了84.9%的现有预测H。pylori蛋白，鉴定了20个新的蛋白质编码基因，并纠正了四个现有的基因模型的翻译起始位点。特别是，GAPP使用相同的蛋白质组学数据揭示了大量的PTM，并提供了丰富的资源，可用于检查这种人类病原体中可逆修饰的功能。该软件是基因组注释和全球发现PTM的强大工具，适用于任何测序的原核生物;我们预计它将成为正在进行的原核生物基因组注释工作的一个组成部分。新闻出版总署可在https://sourceforge.net/projects/gappproteogenomic/上免费查阅。
Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of post-translational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data fromHelicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predictedH. pyloriproteins, identified 20 novel protein coding genes, and corrected four existing gene models with regard to translation initiation sites. In particular, GAPP revealed a large repertoire of PTMs using the same proteomic data and provided a rich resource that can be used to examine the functions of reversible modifications in this human pathogen. This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome annotation efforts for prokaryotes. GAPP is freely available at https://sourceforge.net/projects/gappproteogenomic/.