| 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
run_dbcan proteins.faa protein --out_dir temp/dbcan/${id} --db_dir db/dbcan -t 16
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
