ConSurf 2016:一种用于估计和可视化大分子进化保守性的改进方法。
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.
作者信息
Ashkenazy Haim, Abadi Shiran, Martz Eric, Chay Ofer, Mayrose Itay, Pupko Tal, Ben-Tal Nir
机构信息
Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
出版信息
Nucleic Acids Res. 2016 Jul 8;44(W1):W344-50. doi: 10.1093/nar/gkw408. Epub 2016 May 10.
The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to retain the structural integrity and function of the macromolecule. The ConSurf web server (http://consurf.tau.ac.il), established over 15 years ago, analyses the evolutionary pattern of the amino/nucleic acids of the macromolecule to reveal regions that are important for structure and/or function. Starting from a query sequence or structure, the server automatically collects homologues, infers their multiple sequence alignment and reconstructs a phylogenetic tree that reflects their evolutionary relations. These data are then used, within a probabilistic framework, to estimate the evolutionary rates of each sequence position. Here we introduce several new features into ConSurf, including automatic selection of the best evolutionary model used to infer the rates, the ability to homology-model query proteins, prediction of the secondary structure of query RNA molecules from sequence, the ability to view the biological assembly of a query (in addition to the single chain), mapping of the conservation grades onto 2D RNA models and an advanced view of the phylogenetic tree that enables interactively rerunning ConSurf with the taxa of a sub-tree.
蛋白质中的氨基酸或DNA/RNA中的核酸的进化保守程度反映了其发生突变的自然倾向与维持大分子结构完整性和功能的整体需求之间的平衡。15年前建立的ConSurf网络服务器(http://consurf.tau.ac.il)分析大分子的氨基酸/核酸的进化模式,以揭示对结构和/或功能重要的区域。从查询序列或结构开始,该服务器自动收集同源物,推断它们的多序列比对并重建反映其进化关系的系统发育树。然后在概率框架内使用这些数据来估计每个序列位置的进化速率。在这里,我们为ConSurf引入了几个新功能,包括自动选择用于推断速率的最佳进化模型、对查询蛋白质进行同源建模的能力、从序列预测查询RNA分子的二级结构、查看查询的生物组装(除单链外)的能力、将保守等级映射到二维RNA模型上以及系统发育树的高级视图,该视图允许使用子树的分类群交互式地重新运行ConSurf。