Bacterial Genomics

Genome annotation using Prokka

Introduction

This process uses prokka published in 2014 to annotate a FastA assembly file. It identifies coding sequences (CDS), ribosomal RNAs (rRNA), transfer RNAs (tRNA), and other features. The primary output is a GenBank formatted file.

Alignment/similarity scoring

To boost annotation confidence, we default to an 1e-08 as a similarity e-value cut-off, but this parameter can be modified if a user wishes to relax the homology assignments which could be useful for novel taxa or highly distant homolog matching.

Alternatives

Prokka is meant for rapid annotation, which performs very well in most cases. However, the NCBI’s annotation pipeline “Prokaryotic Genome Annotation Pipeline” (PGAP) is recommended for the most comprehensive annotations, especially if you believe the functional name is to a distant homolog or if the gene of interest appears to be missing in Bakta’s GenBank output file.

PGAP was first developed in 2001 by NCBI and GATech staff and published in 2016. The most recent updates have been reported in 2021.