Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, BC, Canada.
Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada.
Methods Mol Biol. 2024;2836:299-330. doi: 10.1007/978-1-0716-4007-4_16.
Carbohydrates are chemically and structurally diverse, composed of a wide array of monosaccharides, stereochemical linkages, substituent groups, and intermolecular associations with other biological molecules. A large repertoire of carbohydrate-active enzymes (CAZymes) and enzymatic activities are required to form, dismantle, and metabolize these complex molecules. The software SACCHARIS (Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity) provides a rapid, easy-to-use pipeline for the prediction of potential CAZyme function in new datasets. We have updated SACCHARIS to (i) simplify its installation by re-writing in Python and packaging for Conda; (ii) enhance its usability through a new (optional) interactive GUI; and (iii) enable semi-automated annotation of phylogenetic tree output via a new R package or the commonly-used webserver iTOL. Significantly, SACCHARIS v2 has been developed with high-throughput omics in mind, with pipeline automation geared toward complex (meta)genome and (meta)transcriptome datasets to reveal the total CAZyme content ("CAZome") of an organism or community. Here, we outline the development and use of SACCHARIS v2 to discover and annotate CAZymes and provide insight into complex carbohydrate metabolisms in individual organisms and communities.
碳水化合物在化学和结构上具有多样性，由广泛的单糖、立体化学连接、取代基和与其他生物分子的分子间缔合组成。需要大量的碳水化合物活性酶 (CAZymes) 和酶活性来形成、拆解和代谢这些复杂分子。SACCHARIS（用于快速知情预测特异性的碳水化合物活性酶的序列分析和聚类）软件为新数据集的潜在 CAZyme 功能提供了快速、易于使用的预测管道。我们已经更新了 SACCHARIS，以：(i) 通过用 Python 重写和为 Conda 打包来简化其安装；(ii) 通过新的（可选）交互 GUI 提高其可用性；以及 (iii) 通过新的 R 包或常用的网络服务器 iTOL 为系统发育树输出实现半自动注释。重要的是，SACCHARIS v2 是为高通量组学开发的，其管道自动化面向复杂（宏）基因组和（宏）转录组数据集，以揭示生物体或群落的总 CAZyme 含量（“CAZome”）。在这里，我们概述了 SACCHARIS v2 的开发和使用，以发现和注释 CAZymes，并深入了解单个生物体和群落中复杂的碳水化合物代谢。
