biosynthetic-gene-clusters

Similarity networks of biosynthetic gene clusters

BGC Detection and Classification Using Deep Learning

(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.)

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

lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters

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, prophage, etc.) relative to the full genome.

Want to make a neighbourhood-scale synteny plot? Have too many genomic neighbourhoods? SyntenyQC may help!

A tool to remove genomic redundancy from cblaster gene cluster hits

Methods and classes to support Biosynthetic Gene Cluster analysis

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

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 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

metaSMASH - a scalable fork of antiSMASH for metagenome-scale biosynthetic gene cluster (BGC) mining

Facilitates cross-modal retrieval between natural products and biosynthetic gene clusters.

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

Protein structure similarity meets gene clustering mining: find gene clusters from genomically colocalised proteins.

End-to-end bacterial genomics pipeline from FASTQ QC to sequence typing, AMR, plasmid, and virulence detection, and phylogenetic analysis.