GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes | |
Zhang, Jia1; Yang, Ming-kun1; Zeng, Honghui2; Ge, Feng1,2 | |
2016-11-01 | |
Source Publication | MOLECULAR & CELLULAR PROTEOMICS
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ISSN | 1535-9476 |
Volume | 15Issue:11Pages:3529-3539 |
Abstract | 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 from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predicted H. pylori proteins, 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/. |
DOI | 10.1074/mcp.M116.060046 |
Funding Organization | National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China |
Indexed By | SCI |
Language | 英语 |
Funding Project | National Key Research and Development Program[2016YFA0501304] ; National Basic Research Program of China (973 Program)[2012CB518700] ; Chinese Academy of Sciences[XDB14030202] ; National Natural Science Foundation of China[31570829] |
WOS Research Area | Biochemistry & Molecular Biology |
WOS Subject | Biochemical Research Methods |
WOS ID | WOS:000387505500016 |
WOS Keyword | TANDEM MASS-SPECTRA ; PROTEIN-CODING GENES ; FALSE DISCOVERY RATE ; HELICOBACTER-PYLORI ; PROTEOMIC DATA ; PEPTIDE IDENTIFICATION ; ROSEOBACTER CLADE ; GASTRIC-CANCER ; RNA-SEQ ; SPECTROMETRY |
Publisher | AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC |
Funding Organization | National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; National Basic Research Program of China (973 Program) ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China |
Citation statistics | |
Document Type | 期刊论文 |
Identifier | http://ir.ihb.ac.cn/handle/342005/34118 |
Collection | 水生生物分子与细胞生物学研究中心_期刊论文 |
Corresponding Author | Ge, Feng |
Affiliation | 1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Algal Biol, Wuhan 430072, Peoples R China 2.Chinese Acad Sci, Wuhan Branch, Supercomp Ctr, Wuhan, Peoples R China |
Recommended Citation GB/T 7714 | Zhang, Jia,Yang, Ming-kun,Zeng, Honghui,et al. GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes[J]. MOLECULAR & CELLULAR PROTEOMICS,2016,15(11):3529-3539. |
APA | Zhang, Jia,Yang, Ming-kun,Zeng, Honghui,&Ge, Feng.(2016).GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.MOLECULAR & CELLULAR PROTEOMICS,15(11),3529-3539. |
MLA | Zhang, Jia,et al."GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes".MOLECULAR & CELLULAR PROTEOMICS 15.11(2016):3529-3539. |
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