hadeg

name	hadeg
description	HADEG — curated Hydrocarbon Aerobic Degradation Enzymes and Genes database (alkanes, alkenes, aromatics, plastics) plus biosurfactant production genes with experimental evidence. Use to annotate MAG/contig proteins for HC biodegradation and biosurfactant potential. Upstream: https://github.com/jarojasva/HADEG. Route via dom-biosurfactant / microbial-mining. Portal-style BioSurfDB → biosurfdb; glycan DOM → dbcan.
license	MIT
category	analysis-tools
tags	["HADEG","hydrocarbon","biosurfactant","plastic","biodegradation","DOM"]
upstream	https://github.com/jarojasva/HADEG
stage	mining

HADEG

Upstream: jarojasva/HADEG

Citation

Rojas-Vargas, J., Castelán-Sánchez, H. G. & Pardo-López, L. HADEG: A curated hydrocarbon aerobic degradation enzymes and genes database. Comput. Biol. Chem. 107, 107966 (2023). https://doi.org/10.1016/j.compbiolchem.2023.107966

See also docs/references.md.

Analytical thinking

HADEG provides experimentally supported sequences for:

• Alkanes / alkenes / aromatics (aerobic HC degradation)
• Plastics / polymer degradation
• Biosurfactant production

Annotate proteomes (e.g. DIAMOND / Proteinortho patterns in upstream README). Pin the HADEG FASTA release date — the GitHub DB grows over time.

vs	Prefer HADEG when
biosurfdb	Offline curated FASTA annotation vs portal BLAST
dbcan	HC/surfactant/plastic genes vs glycan CAZymes
antismash	Marker-gene presence vs full BGC regions

How to run

# download HADEG_protein_database_*.faa from upstream releases
# typical: diamond blastp -q proteins.faa --db HADEG.dmnd -o hits.tsv …
# or Proteinortho workflows in upstream README; then parse group tables
# (Alkanes / Alkenes / Aromatics / Biosurfactants / Plastics)

Decision tree

HC / plastic / biosurfactant genes?
├─ Curated experimental set → hadeg
├─ BioSurfDB portal pathways → biosurfdb
├─ Glycan DOM → dbcan
└─ Surfactant BGCs → antismash

Related skills

dom-biosurfactant · biosurfdb · dbcan · antismash · dram · microbial-mining · tool-selection