Glanville Jake Gunn, Kirshner Dan, Krishnamurthy Nandini, Sjölander Kimmen
Berkeley Phylogenomics Group, University of California, Berkeley, USA.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W27-32. doi: 10.1093/nar/gkm325. Epub 2007 May 8.
Phylogenomic analysis addresses the limitations of function prediction based on annotation transfer, and has been shown to enable the highest accuracy in prediction of protein molecular function. The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction and SCI-PHY subfamily identification. The PhyloBuilder web server provides an integrated phylogenomic pipeline starting with a user-supplied protein sequence, proceeding to homolog identification, multiple alignment, phylogenetic tree construction, subfamily identification and structure prediction. The Berkeley Phylogenomics Group resources are available at http://phylogenomics.berkeley.edu.
系统发育基因组学分析解决了基于注释转移的功能预测的局限性，并且已被证明能够在蛋白质分子功能预测中实现最高的准确性。伯克利系统发育基因组学小组提供了一系列用于系统发育基因组学分析的网络服务器：使用系统发育事实系统发育基因组学百科全书将序列分类到预先计算的家族和亚家族中，对具有相同结构域结构的蛋白质进行花之力聚类，进行MUSCLE多序列比对、SATCHMO同时比对和树构建以及SCI-PHY亚家族鉴定。PhyloBuilder网络服务器提供了一个集成的系统发育基因组学流程，从用户提供的蛋白质序列开始，进行同源物鉴定、多序列比对、系统发育树构建、亚家族鉴定和结构预测。伯克利系统发育基因组学小组的资源可在http://phylogenomics.berkeley.edu获取。
