IHB OpenIR  > 水生生物分子与细胞生物学研究中心  > 期刊论文
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 PublicationMOLECULAR & CELLULAR PROTEOMICS
ISSN1535-9476
Volume15Issue: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/.

DOI10.1074/mcp.M116.060046
Funding OrganizationNational 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 BySCI
Language英语
Funding ProjectNational 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 AreaBiochemistry & Molecular Biology
WOS SubjectBiochemical Research Methods
WOS IDWOS:000387505500016
WOS KeywordTANDEM MASS-SPECTRA ; PROTEIN-CODING GENES ; FALSE DISCOVERY RATE ; HELICOBACTER-PYLORI ; PROTEOMIC DATA ; PEPTIDE IDENTIFICATION ; ROSEOBACTER CLADE ; GASTRIC-CANCER ; RNA-SEQ ; SPECTROMETRY
PublisherAMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
Funding OrganizationNational 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
Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://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 AuthorGe, Feng
Affiliation1.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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