Deluca Todd F, Wu I-Hsien, Pu Jian, Monaghan Thomas, Peshkin Leonid, Singh Saurav, Wall Dennis P
The Center for Biomedical Informatics & Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
Bioinformatics. 2006 Aug 15;22(16):2044-6. doi: 10.1093/bioinformatics/btl286. Epub 2006 Jun 15.
We have created a tool for ortholog and phylogenetic profile retrieval called Roundup. Roundup is backed by a massive repository of orthologs and associated evolutionary distances that was built using the reciprocal smallest distance algorithm, an approach that has been shown to improve upon alternative approaches of ortholog detection, such as reciprocal blast. Presently, the Roundup repository contains all possible pair-wise comparisons for over 250 genomes, including 32 Eukaryotes, more than doubling the coverage of any similar resource. The orthologs are accessible through an intuitive web interface that allows searches by genome or gene identifier, presenting results as phylogenetic profiles together with gene and molecular function annotations. Results may be downloaded as phylogenetic matrices for subsequent analysis, including the construction of whole-genome phylogenies based on gene-content data.
我们创建了一个名为Roundup的直系同源基因和系统发育谱检索工具。Roundup有一个庞大的直系同源基因库及相关进化距离作为支撑，该基因库是使用相互最小距离算法构建的，这种方法已被证明比直系同源基因检测的其他方法（如相互比对）更具优势。目前，Roundup基因库包含了超过250个基因组的所有可能的成对比较，其中包括32个真核生物，比任何类似资源的覆盖范围增加了一倍多。可通过直观的网络界面访问直系同源基因，该界面允许按基因组或基因标识符进行搜索，并将结果呈现为系统发育谱以及基因和分子功能注释。结果可以作为系统发育矩阵下载，用于后续分析，包括基于基因含量数据构建全基因组系统发育树。
