BGC Detection and Classification Using Deep Learning

Similarity networks of biosynthetic gene clusters

(Meta-)genome screening for functional and natural product gene sequences

GEne Cluster prediction with COnditional random fields.

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters

Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)

lsaBGC - suite for pan-BGC-omics analysis

codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.

Methods and classes to support Biosynthetic Gene Cluster analysis

The Functional Order (FunOrder) tool - Identification of essential biosynthetic genes through computational molecular co-evolution – novel tool that allows automated identification of essential genes in a biosynthetic gene clusters (BGC) based solely on genomic data

Repository for data, code & figures related to the publication: "Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic"

Repository of the paper "Exploring sequence landscape of biosynthetic gene clusters with protein language models" published at ICML2024 workshop Machine Learning for Life and Material Science: From Theory to Industry applications

Parse binary files from NCBI blast or Cblaster into more useful information (tree, table and pie chart)

Case studies of reproducibility in bioinformatics: Metabolomics

An R shinny app for Substructure Search in MIBiG database.

This is a BioDIGS in the Classroom companion guide for the BioDIGS project. This particular activity guides students through exploration of biosynthetic gene clusters in the BioDIGS samples using Galaxy

A Graphical User Interface to Access and Output Protein Data

This repo is for the scripts used in preparation of Flongle Actinomycetes paper