LAB Genomics Suite: Integrated tools for functional and safety evaluation of Lactic Acid Bacteria

This repository contains the computational suite developed for the study: "Integrated genome-based and in vivo safety evaluation of Lactiplantibacillus plantarum M2". The suite comprises two specialized tools for the analysis of Lactic Acid Bacteria (LAB) genomes annotated with BAKTA: LAB Functional Profiler (Web interface): A Streamlit-based application for comparative functional profiling. It features automated normalization (per 1,000 CDS) and strict operon-completeness validation to prevent biological overestimation. Biogenic Amine Screener (Command-line): A rigorous screening pipeline for biogenic amine (BA) biosynthetic pathways. It utilizes pathway-based validation and specific exclusion filters for metabolic homologs (e.g., argJ, ldcA) to ensure high-confidence biosafety results. Requirements Python 3.9+ Dependencies: pandas, numpy, seaborn, matplotlib, scipy, streamlit, xlsxwriter Installation Clone the repository and install the required packages: git clone https://github.com/YourUsername/LAB-Genomics-Suite.git cd LAB-Genomics-Suite pip install -r requirements.txt