Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.
APC Microbiome Ireland, University College Cork, Cork, Ireland.
Microb Genom. 2024 Feb;10(2). doi: 10.1099/mgen.0.001183.
Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on specific members of that family. Using a previously gathered dataset of more than 280 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3) family, we evaluated the efficiency of different databases and search tools, and devised a workflow that experimentalists can use to capture the most information published on members of a protein family in the least amount of time. To complement this workflow, web-based platforms allowing for the exploration of protein family members across sequenced genomes or for the analysis of gene neighbourhood information were reviewed for their versatility and ease of use. Recommendations that can be used for experimentalist users, as well as educators, are provided and integrated within a customized, publicly accessible Wiki.
捕获给定蛋白质家族所有成员的已发表文献信息，应该是任何聚焦于该家族特定成员的研究的基本步骤。我们使用之前收集的一个包含 280 多个参考文献的数据集，这些参考文献都提到了 DUF34（NIF3/Ngg1 相互作用因子 3）家族的一个成员，评估了不同数据库和搜索工具的效率，并设计了一个工作流程，实验人员可以使用该流程在最短的时间内捕获到关于蛋白质家族成员的最多已发表信息。为了补充这个工作流程，我们还对允许跨测序基因组探索蛋白质家族成员或分析基因邻域信息的基于网络的平台进行了评估，以了解它们的多功能性和易用性。我们提供了可用于实验人员用户以及教育工作者的建议，并将其整合到一个定制的、可公开访问的 Wiki 中。
