akulikova64 / microcin_embeddings_project

Semantic search using protein large language models detects class II microcins in bacterial genomes

This repository contains code for microcin search, analysis and additional data.

distance_csvs/ - csv files that contain embedding distances between 10 known microcin embeddings and ORFs

BLAST_results/ - blast results

analysis/figures/ - contains all plots and figures with distances

src/ - R and python scripts for data processing

Scripts for data preparation:

1. python/run_pipeline2.py - pipeline for microcin search. It extracts ORFs, filters ORFs, annotates known microcin ORFs, runs esm1-b to generate embeddings, calculates semantic distance with known microins and averaged microcin embedding.

2. python/run_blastp.py - Runs protein blast using the 10 known microcins sequences as queries.

Scripts for analysis:

1. R/genome_template_emb.Rmd - template for data analysis for a single genome/assembly

2. R/microcin_homology_plots.Rmd - code for Figure 5 in paper

---

CC BY-NC 4.0 This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (see https://creativecommons.org/licenses/by-nc/4.0/legalcode).

Using this work commercially may require a license to intellectual property owned by the Board of Regents of the University of Texas System. Contact [e-mail] for inquiries.