dbcan

name	dbcan
description	Annotate carbohydrate-active enzymes (CAZymes) with dbCAN3 / run_dbcan on genomes or protein sets, including CGC finding and glycan substrate prediction (dbCAN-sub / dbCAN-PUL) relevant to dissolved organic matter (DOM) polymer processing. Use for CAZyme mining complementary to DRAM/eggNOG and to dom-biosurfactant routing. Upstream: https://github.com/linnabrown/run_dbcan.
license	MIT
category	analysis-tools
tags	["CAZy","CAZyme","DOM","glycan","substrate","genome-mining","dbCAN3"]
upstream	https://github.com/linnabrown/run_dbcan
stage	mining

dbCAN (run_dbcan / dbCAN3)

Upstream: linnabrown/run_dbcan · Server: https://bcb.unl.edu/dbCAN2/

Citation

Zheng, J. et al. dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res. 51, W115–W121 (2023). https://doi.org/10.1093/nar/gkad328

Earlier: Zhang, H. et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46, W95–W101 (2018). https://doi.org/10.1093/nar/gky418

See also docs/references.md.

Analytical thinking

CAZymes process complex carbohydrates — a major fraction of DOM / polymer organic matter (cellulose, xylan, pectin, mucin, etc.). dbCAN3 adds substrate prediction at subfamily and CGC/PUL levels. Prefer protein FASTA (+ GFF for CGC) from bakta/prodigal. Consensus across HMMER/DIAMOND/ dbCAN-sub is stronger than a single hit.

vs	Prefer dbCAN when
hadeg / biosurfdb	Glycan DOM vs HC/biosurfactant genes
dram	Dedicated CAZyme/substrate detail vs distillate sheets
element-cycling	Organic C polymer enzymes vs inorganic C/N/S cycles

How to run

# Follow upstream for DB download (dbCAN HMM, CAZy, dbCAN-sub, PUL, …)
run_dbcan proteins.faa protein --out_dir temp/dbcan/${id} --db_dir db/dbcan -t 16
# CGC + substrate: supply GFF / use substrate_prediction per run_dbcan docs

Decision tree

Glycan / DOM polymer capacity?
├─ CAZymes + substrates / CGC → dbcan
├─ HC / biosurfactant / plastic → hadeg (± biosurfdb)
├─ Broad distillate → dram
└─ Route menu → dom-biosurfactant

Related skills

dom-biosurfactant · hadeg · biosurfdb · dram · eggnog-mapper · bakta · prodigal · element-cycling · microbial-mining · tool-selection