Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
NGS Competence Center Tübingen, Tübingen, Germany.
J Comput Biol. 2023 Sep;30(9):999-1008. doi: 10.1089/cmb.2023.0156. Epub 2023 Aug 25.
Identifying a protein's function is crucial to reveal its role in the cellular complex. Computationally, the most common approach is to search for homologous proteins in a large database of proteins of known function using BLAST. One goal of such an analysis is the identification and visualization of the protein in the taxonomy of interest. Another goal is the reconstruction of the phylogenetic history of the protein. However, the BLAST result provides information about the occurrence of the protein in the taxonomy and its putative function mainly in a tabular format. This requires manual interventions and makes the taxonomic identification laborious. Although various tools exist to visualize and annotate large-scale trees, none of them intuitively and interactively visualizes the protein's occurrence in the taxonomy for different taxonomic ranks. To target this gap, we developed BLASTphylo, a web tool that combines BLAST with automatic taxonomic mapping and phylogenetic analysis and provides the results in interactive visualizations. We demonstrate the functionalities of BLASTphylo in two case studies.
确定蛋白质的功能对于揭示其在细胞复合物中的作用至关重要。在计算上，最常用的方法是使用 BLAST 在具有已知功能的大型蛋白质数据库中搜索同源蛋白质。此类分析的一个目标是识别和可视化感兴趣分类单元中的蛋白质。另一个目标是重建蛋白质的系统发育历史。然而，BLAST 结果主要以表格形式提供关于蛋白质在分类单元中的出现及其假定功能的信息。这需要手动干预，使得分类鉴定变得繁琐。尽管存在各种用于可视化和注释大规模树的工具，但它们都没有直观和交互式地可视化蛋白质在不同分类等级中的出现情况。为了针对这一差距，我们开发了 BLASTphylo，这是一种将 BLAST 与自动分类映射和系统发育分析相结合的网络工具，并以交互式可视化方式提供结果。我们在两个案例研究中演示了 BLASTphylo 的功能。
