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While 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 posttranslational 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.