Preparing Databases

Preparing Databases#

Database files are essential for running dbCAN analysis. This guide explains how to install and prepare these databases.

Automatic Database Installation#

The simplest way to obtain all required databases is using the built-in command in run_dbCAN:

run_dbcan database --db_dir db

To download from AWS S3 (faster and more stable in many regions), add the --aws_s3 flag:

run_dbcan database --db_dir db --aws_s3

To download only CAZyme-related databases (without CGC-related databases), use --no-cgc:

run_dbcan database --db_dir db --no-cgc

This command will automatically download all necessary databases and organize them in the specified directory. The default HTTP source points at the moving db_current snapshot. The --aws_s3 source points at the pinned db_v5-2_9-13-2025 release, which is preferable when you need reproducible database contents across machines.

For unreliable networks, the downloader also supports retry and resume controls:

run_dbcan database --db_dir db --aws_s3 --timeout 60 --retries 5 --resume

Use --no-overwrite to keep existing files untouched. By default, existing files may be checked by remote size and completed partial downloads are resumed when possible.

Tip

We recommend creating a dedicated directory for databases, as they will be reused for multiple analyses.

Manual Database Installation#

If you prefer to download database files manually or face connectivity issues, use the same paths as the built-in downloader. The HTTP source is:

https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/<filename>

The pinned S3 source is:

https://dbcan.s3.us-west-2.amazonaws.com/db_v5-2_9-13-2025/<filename>

Step-by-Step Instructions:

  1. Create a database directory:

    mkdir -p db && cd db

  2. Download the required database files:

    # CAZyme databases
wget -O CAZy.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/CAZy.dmnd"
wget -O dbCAN.hmm "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/dbCAN.hmm"
wget -O dbCAN-sub.hmm "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/dbCAN_sub.hmm"
wget -O fam-substrate-mapping.tsv "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/fam-substrate-mapping.tsv"

# CGC-related databases
wget -O TCDB.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/TCDB.dmnd"
wget -O TF.hmm "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/TF.hmm"
wget -O TF.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/TF.dmnd"
wget -O STP.hmm "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/STP.hmm"
wget -O PUL.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/PUL.dmnd"
wget -O dbCAN-PUL.xlsx "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/dbCAN-PUL.xlsx"
wget -O dbCAN-PUL.tar.gz "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/dbCAN-PUL.tar.gz"
wget -O peptidase_db.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/peptidase_db.dmnd"
wget -O sulfatlas_db.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/sulfatlas_db.dmnd"

tar -xzf dbCAN-PUL.tar.gz

  3. Verify your downloads:

    ls -lh
# You should see CAZy.dmnd, dbCAN.hmm, dbCAN-sub.hmm, fam-substrate-mapping.tsv, and other files.

Note

For a complete list of required database files and their descriptions, please visit the dbCAN2 database documentation.

Testing Your Installation#

After installing the databases, you can verify your setup using example files from our test data repository.

Next Steps

Once your databases are installed, proceed to the CAZyme Annotation section to start analyzing your sequences.

Contents