title: GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.
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/.
authors.affiliation: From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Zhang
authors.affiliation: From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Ming-Kun
authors.initials: MK
authors.lastname: Yang
authors.affiliation: §Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China.
authors.forename: Honghui
authors.initials: H
authors.lastname: Zeng
authors.affiliation: From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; gefeng@ihb.ac.cn.|§Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Ge
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D058977:Molecular Sequence Annotation; D011499:Protein Processing, Post-Translational; D000071696:Proteogenomics / Q000379:methods*; D012984:Software
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins