Code repository for the AssayBLAST v2 publication

This repository hosts results from the AssayBLAST v2 publication and code to reproduce these.

Accession numbers can be found in data/organisms.json and assay/microarray_results.txt.

Prerequisites: conda installation using conda-forge and bioconda channels.

First, please install the necessary packages:

conda create -n assayblast_paper "python=3.14" "blast=2.17.0" matplotlib numpy pandas seaborn scipy "biopython=1.85"
conda activate assayblast_paper
pip install "rnajena-sugar==1.1" "assay_blast==2.4"

Create the example result tables (tables 2, 3)

The overview and details tables are located in the example folder. To re-create them switch to the example folder and run the following commands.

assay_test -d .
assay_blast example_database.fasta -q example_queries.fasta --mismatch 2
assay_analyze blast_results.tsv --mismatch 2

Analyze score to bit score relationship (figure 1)

The first script downloads the genomes. The second script calculates the bit scores and plots the relationship.

python prepare_genomes.py
python bitscore_vs_score.py

Comparison to AssayBLAST v1.0 (tables 4, 5)

This section requires the genomes downloaded in the previous section. We download AssayBLAST v1.0 from GitHub and create a modified version with a fixed E-value of 1000. The script evaluation.py runs the different AssayBLAST versions with various primers and organisms and generates the comparison table.

git clone --branch v1.0 https://github.com/rnajena/AssayBLAST.git AssayBLASTv1
sed 's/evalue=100000/evalue=1000/g' AssayBLASTv1/assayBLAST.py > AssayBLASTv1/assayBLAST_e1k.py
python evaluation.py

Comparison with Microarray assay (figure 3)

The microarray_results.txt and primer_and_probe.fasta files were obtained from the supplementary material of Collatz et al. (2025, doi).

The following code downloads the corresponding genomes, executes AssayBLAST v2, and generates the confusion matrix.

python assay_evaluation_prepare.py
cd assay
assay_blast -q primer_and_probe.fasta genomes.fasta
assay_analyze blast_results.tsv --distance 150
cd ..
python assay_evaluation_analyze.py