The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Pipeline was developed in 2001 and is regularly upgraded to improve structural and functional annotation quality (Haft DH et al 2018, Tatusova T et al 2016). Recent improvements utilize curated protein profile hidden Markov models (HMMs), including TIGRFAMS and new HMMs for antimicrobial resistance proteins, and curated complex domain architectures for functional annotation of proteins.
The annotation pipeline for NCBI which includes automatic annotation based on homology.
The service has specific format requirements based on the sequence submitted, make sure to follow the instructions.