Step 1: Bidirectional BLAST

The first step of the workflow is to perform a bidirectional BLAST using DIAMOND on the input and template genomes. The aim is to identify genes that are found in both genomes. The bidirectional BLAST ensures a high certainty value. The idea is based on the workflow described by Norsigian et al.[1].

Below is an overview of this step of the workflow:

[1]

Charles J Norsigian, Xin Fang, Yara Seif, Jonathan M Monk, and Bernhard O Palsson. A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. Nature protocols, 15(1):1–14, 2020.