commec: a free, open-source, globally available tool for DNA sequence screening

The commec package is a tool for DNA sequence screening that is part of the Common Mechanism for DNA Synthesis screening.

Introduction : Common Mechanism Databases

The Common Mechanism offers DNA sequence screening: The screen command runs an input FASTA through four steps:

1. Biorisk scan (uses a hmmer search against custom databases)
2. Regulated protein scan (uses a BLASTX or DIAMOND search against NCBI nr)
3. Regulated nucleotide scan (uses BLASTN against NCBI nt)
4. Benign scan (users hmmer, cmscan and BLASTN against custom databases)

This repository contains the Biorisk and Benign database files necessary for steps 1 and 4. These are the only databases necessary when running Commec in the truncated --skip-tx mode where regulated taxonomy steps are skipped.

These files can be downloaded to a desired location using the commec setup command line interface. Alternatively, downloading commec-dbs.zip from the a tagged release, and placing the extracted files in a location to be pointed to with the -d, --databases commec cli. Or ensure that the yaml parameters file points to the biorisk and benign directories respectively.

Database Release and Update

Updating the databases will entail the following steps:

• Ensure git lfs is installed, and pull using git lfs pull
• Update the relevant files inside the commec-dbs sub-directory within the repo.
• Create a Pull Request for changes into main, this will trigger unit tests on the database files.
• On a successfully merged pull request, merge into main.
• Use the tag and release github action, supply the semantic version, which will automate the release.

About

The Common Mechanism is a project of IBBIS, the International Biosecurity and Biosafety Initiative for Science. From 2021-2023, the software and databases were developed by a team of technical consultants working with the Nuclear Threat Initiative, led by Dr. Nicole Wheeler of the University of Birmingham, and including contributions from Brittany Rife Magalis of the University of Louisville and Jennifer Lu of the Center for Computational Biology at Johns Hopkins University. In 2024, IBBIS became the home of the project.