Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
LLa-BioEconomy, Research & Advisory, 2500 Valby, Denmark.
Nucleic Acids Res. 2020 Jul 2;48(W1):W110-W115. doi: 10.1093/nar/gkaa375.
The CUPP platform includes a web server for functional annotation and sub-grouping of carbohydrate active enzymes (CAZymes) based on a novel peptide-based similarity assessment algorithm, i.e. protein grouping according to Conserved Unique Peptide Patterns (CUPP). This online platform is open to all users and there is no login requirement. The web server allows the user to perform genome-based annotation of carbohydrate active enzymes to CAZy families, CAZy subfamilies, CUPP groups and EC numbers (function) via assessment of peptide-motifs by CUPP. The web server is intended for functional annotation assessment of the CAZy inventory of prokaryotic and eukaryotic organisms from genomic DNA (up to 30MB compressed) or directly from amino acid sequences (up to 10MB compressed). The custom query sequences are assessed using the CUPP annotation algorithm, and the outcome is displayed in interactive summary result pages of CAZymes. The results displayed allow for inspection of members of the individual CUPP groups and include information about experimentally characterized members. The web server and the other resources on the CUPP platform can be accessed from https://cupp.info.
CUPP 平台包括一个基于新型肽基相似性评估算法（即根据保守独特肽模式（CUPP）对蛋白质进行分组）的功能注释和碳水化合物活性酶（CAZymes）亚组划分的网络服务器。该在线平台对所有用户开放，无需登录。该网络服务器允许用户通过 CUPP 对肽基序进行评估，从而对碳水化合物活性酶进行基于基因组的 CAZy 家族、CAZy 亚家族、CUPP 组和 EC 编号（功能）注释。该网络服务器用于对来自基因组 DNA（最多 30MB 压缩）或直接来自氨基酸序列（最多 10MB 压缩）的原核和真核生物的 CAZy 清单进行功能注释评估。使用 CUPP 注释算法评估自定义查询序列，结果显示在 CAZymes 的交互式摘要结果页面中。显示的结果允许检查各个 CUPP 组的成员，并包含有关经过实验表征的成员的信息。可以从 https://cupp.info 访问 CUPP 平台的网络服务器和其他资源。
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