dbCAN database

Introduction

dbCAN3 server is a web server for automated Carbohydrate-active enzyme ANnotation (Zheng et al. 2023). This webserver allows users predict glycan substrates for CAZymes by searching against dbCAN-sub, and for CAZyme gene clusters (CGCs). You can submit data for entire genomes or proteomes, however, you can also use the dbDAN HMM database as outlined below. This database is based on the Carbohydrate-Active enZYmes Database (CAZy).

Installation

Available on crunchomics: Yes,

• The dbCAN database is installed as part of the bioinformatics share. If you have access to crunchomics and have not yet access to the bioinformatics you can send an email with your Uva netID to Nina Dombrowski.

The database can be found here:

• /zfs/omics/projects/bioinformatics/databases/dbCAN.

If you want to download the database yourself, you can do:

# Download database and mapping file 
wget http://dbcan-hcc.unl.edu/download/dbCAN-HMMdb-V14.txt
wget http://dbcan-hcc.unl.edu/download/Databases/fam-substrate-mapping-08262025.tsv

# Clean mapping file
sed -i 's/ /_/g' fam-substrate-mapping-08262025.tsv

Example usage

The database can be searched with hmmsearch and we provide a small python script to parse the output:

## Run search
hmmsearch \
    --tblout results/sequence_results.txt \
    --domtblout results/domain_results.txt \
    --notextw \
    --cpu 4 \
    /zfs/omics/projects/bioinformatics/databases/dbCAN/dbCAN-HMMdb-V14.txt \
    GCF_000970205.faa

## Parse the result (example)
python /zfs/omics/projects/bioinformatics/databases/dbCAN/parse_dbCAN.py  \
    -i results/domain_results.txt \
    -m /zfs/omics/projects/bioinformatics/databases/dbCAN/fam-substrate-mapping-08262025.tsv \
    -o results \
    -e 1e-5 -c 0.30

The python script filters by E-value and coverage, removes overlapping domains, and provides both detailed and summary outputs. It has the following options:

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input hmmsearch domtblout file
  -m METADATA, --metadata METADATA
                        dbCAN family-substrate mapping file (TSV)
  -o OUTDIR, --outdir OUTDIR
                        Output directory for results
  -e EVALUE, --evalue EVALUE
                        E-value threshold for filtering hits
                        Default: 1e-15
  -c COVERAGE, --coverage COVERAGE
                        Coverage threshold for filtering hits (0-1)
                        Default: 0.35
  --overlap-threshold OVERLAP_THRESHOLD
                        Overlap threshold for removing redundant hits (0-1)
                        Default: 0.5

References

Zheng, Jinfang, Qiwei Ge, Yuchen Yan, Xinpeng Zhang, Le Huang, and Yanbin Yin. 2023. “dbCAN3: Automated Carbohydrate-Active Enzyme and Substrate Annotation.” Nucleic Acids Research 51 (W1): W115–21. https://doi.org/10.1093/nar/gkad328.