Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix, Singapore 138671.
Nucleic Acids Res. 2012 Jan;40(Database issue):D490-4. doi: 10.1093/nar/gkr1129. Epub 2011 Dec 1.
Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. The analysis is organized around the nomenclature associated with the human proteins, but based on all currently available vertebrate genomes. Using full genomes enables us, through a mutual-best-hit strategy, to construct comparable taxonomical samples for all paralogues under consideration. Functional specialization is scored on the residue level according to two models of behavior after divergence: heterotachy and homotachy. In the first case, the positions on the protein sequence are scored highly if they are conserved in the reference group of orthologs, and overlap poorly with the residue type choice in the paralogs groups (such positions will also be termed functional determinants). The second model additionally requires conservation within each group of paralogs (functional discriminants). The scoring functions are phylogeny independent, but sensitive to the residue type similarity. The results are presented as a table of per-residue scores, and mapped onto related structure (when available) via browser-embedded visualization tool. They can also be downloaded as a spreadsheet table, and sessions for two additional molecular visualization tools. The database interface is available at http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html.
Cube-DB 是一个预先评估的人类/脊椎动物蛋白质家族功能分化检测结果的数据库。该分析围绕着与人类蛋白质相关的命名法展开，但基于所有现有的脊椎动物基因组。使用完整的基因组，我们通过一种相互最佳匹配的策略，为所有考虑的同源物构建可比的分类学样本。功能特化在残基水平上根据分歧后的两种行为模型进行评分：异速进化和同速进化。在第一种情况下，如果蛋白质序列上的位置在同源物参考组中保守，并且与同源物组中的残基类型选择重叠较少，则这些位置的得分较高（这些位置也将被称为功能决定因素）。第二种模型还要求在每个同源物组内保守（功能鉴别因子）。评分函数与系统发育无关，但对残基类型相似性敏感。结果以每残基得分表的形式呈现，并通过浏览器嵌入式可视化工具映射到相关结构（如果可用）。它们也可以下载为电子表格表，并用于另外两个分子可视化工具的会话。数据库接口可在 http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html 获得。
