NCBI prokaryotic genome annotation pipeline

Advances in sequencing have made it possible to analyze populations of pathogenic species during disease outbreaks and to study diversity across the whole prokaryotic domain, creating a need for timely, comprehensive automatic genome annotation. Developed by NCBI in collaboration with Georgia Tech, the Prokaryotic Genome Annotation Pipeline (PGAP) combines alignment-based methods with methods that predict protein-coding genes, RNA genes, and other functional elements directly from sequence. A gene-finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial annotation map to generate and modify ab initio gene predictions across the whole genome.

The pipeline is designed to lean more on sequence similarity when confident comparative data are available and more on statistical predictions when external evidence is absent, balancing the two sources of information. This design gives PGAP a framework capable of generating and analyzing annotation across the full breadth of prokaryotic taxonomy, supporting both outbreak interpretation and broad diversity studies.