Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris 75005, France.
Sorbonne Université, CNRS, Institut des Sciences du Calcul et des Données (ISCD), France.
Nucleic Acids Res. 2021 Jul 2;49(W1):W452-W458. doi: 10.1093/nar/gkab395.
The ever-increasing number of genomic and metagenomic sequences accumulating in our databases requires accurate approaches to explore their content against specific domain targets. MyCLADE is a user-friendly webserver designed for targeted functional profiling of genomic and metagenomic sequences based on a database of a few million probabilistic models of Pfam domains. It uses the MetaCLADE multi-source domain annotation strategy, modelling domains based on multiple probabilistic profiles. MyCLADE takes a list of protein sequences and possibly a target set of domains/clans as input and, for each sequence, it provides a domain architecture built from the targeted domains or from all Pfam domains. It is linked to the Pfam and QuickGO databases in multiple ways for easy retrieval of domain and clan information. E-value, bit-score, domain-dependent probability scores and logos representing the match of the model with the sequence are provided to help the user to assess the quality of each annotation. Availability and implementation: MyCLADE is freely available at http://www.lcqb.upmc.fr/myclade.
我们的数据库中积累的基因组和元基因组序列数量不断增加，这就需要准确的方法来针对特定的领域目标来探索它们的内容。MyCLADE 是一个用户友好的网络服务器，专为基于 Pfam 域的数百万个概率模型数据库对基因组和元基因组序列进行靶向功能分析而设计。它使用 MetaCLADE 多源域注释策略，基于多个概率分布来对域进行建模。MyCLADE 以蛋白质序列列表和可能的目标域/族集作为输入，对于每个序列，它都提供一个由目标域或所有 Pfam 域构建的域结构。它通过多种方式与 Pfam 和 QuickGO 数据库链接，以便于检索域和族信息。提供 E 值、位得分、与序列匹配的模型的域相关概率评分和徽标，以帮助用户评估每个注释的质量。可用性和实现：MyCLADE 可免费在 http://www.lcqb.upmc.fr/myclade 获得。
