PKG-INFO

Metadata-Version: 2.1
Name: dbcan
Version: 4.1.4
Summary: Standalone version of dbCAN annotation tool for automated CAZyme annotation
Project-URL: Documentation, https://dbcan.readthedocs.io/
Project-URL: Source, https://github.com/linnabrown/run_dbcan/
Project-URL: Home-page, https://bcb.unl.edu/dbCAN2/
Author: Le Huang, Jinfang Zheng, Haidong Yi, Qiwei Ge, Tanner Yohe
Maintainer-email: Le Huang <lehuang@unc.edu>, Haidong Yi <haidyi@cs.unc.edu>
License:                     GNU GENERAL PUBLIC LICENSE
                               Version 3, 29 June 2007
        
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Description-Content-Type: text/markdown

[![dbcan](https://github.com/linnabrown/run_dbcan/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/linnabrown/run_dbcan/actions/workflows/ci.yml)
[![Documentation Status](https://readthedocs.org/projects/dbcan/badge/?version=latest)](https://dbcan.readthedocs.io/en/latest/?badge=latest)
[![Package status](https://anaconda.org/bioconda/dbcan/badges/version.svg)](https://anaconda.org/bioconda/dbcan)
[![GitHub license](https://img.shields.io/badge/license-GNU3.0-blue.svg)](https://github.com/linnabrown/run_dbcan/blob/master/LICENSE)
[![Platform](https://anaconda.org/bioconda/dbcan/badges/platforms.svg)](https://anaconda.org/bioconda/dbcan/badges/platforms.svg)
[![GitHub downloads](https://anaconda.org/bioconda/dbcan/badges/downloads.svg)](https://anaconda.org/bioconda/dbcan)
[![GitHub versions](https://img.shields.io/pypi/pyversions/dbcan.svg)](https://anaconda.org/bioconda/dbcan)

# run_dbcan - Standalone Tool of [dbCAN3](http://bcb.unl.edu/dbCAN2/)

**run_dbcan** is the standalone version of the [dbCAN3](http://bcb.unl.edu/dbCAN2/) 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](https://github.com/linnabrown/run_dbcan/issues). 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](https://doi.org/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](https://doi.org/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\*](https://doi.org/10.1093/nar/gkx894*).

[dbcan doc]: https://dbcan.readthedocs.io