run_dbcan - Standalone Tool of dbCAN3

Update

5/12/2025: dev-dbcan branch is used to test new functions and fix issues. After testing, this branch will be merged into the main branch and update docker/conda/pypi. If you want to use those beta functions, please replace the code folder (dbcan) with your current package.

3/16/2025: 1. Rewrite the structure of rundbcan 4.0 (suggested by Haidong), using object-oriented programming (OOP) to improve maintainability and readability. 2. Added new function: cgccircle, which can visualize CGC in genome.

Future plans Add prediction of food consumption through CAZyme. If you have new suggestions, please contact Dr. Yanbin Yin (yyin@unl.edu), Xinpeng Zhang (xzhang55@huskers.unl.edu), and Dr. Haidong Yi (hyi@stjude.org).

Introduction

Notice

This is the updated version of rundbcan 4.0. Many changes have been made and described in https://run-dbcan.readthedocs.io/en/latest/. From now on, this repo is the official rundbcan site, and the site at run_dbcan 4.0 will be no longer maintained.

run_dbcan is the standalone version of the dbCAN3 annotation tool for automated CAZyme annotation. This tool, known as run_dbcan, incorporates HMMER, Diamond, and dbCAN_sub for annotating CAZyme families, and integrates Cazyme Gene Clusters (CGCs) and substrate predictions.

For usage discussions, visit our issue tracker. To learn more, read the dbcan doc. If you're interested in contributing, whether through issues or pull requests, please review our contribution guide.

Reference

Please cite the following dbCAN publications if you use run_dbcan in your research:

dbCAN3: automated carbohydrate-active enzyme and substrate annotation

Jinfang Zheng, Qiwei Ge, Yuchen Yan, Xinpeng Zhang, Le Huang, Yanbin Yin,

Nucleic Acids Research, 2023;, gkad328, doi: 10.1093/nar/gkad328.

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter K Busk, Ying Xu, Yanbin Yin

Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W95–W101, doi: 10.1093/nar/gky418.

dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation

Le Huang, Han Zhang, Peizhi Wu, Sarah Entwistle, Xueqiong Li, Tanner Yohe, Haidong Yi, Zhenglu Yang, Yanbin Yin

Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D516–D521, doi: 10.1093/nar/gkx894*.