Zhou Yi, Landweber Laura F
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W678-82. doi: 10.1093/nar/gkm278. Epub 2007 May 5.
We present BLAST on Orthologous groups (BLASTO), a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences. By filtering out redundancy and putative paralogs, sequence comparisons to orthologous groups, instead of to single sequences in the database, can improve both functional prediction and phylogenetic inference. BLASTO computes the significance score of each orthologous group based on the individual BLAST hits in the orthologous group, using the number of taxa in the group as an optional weight. This allows users to control the species diversity of the orthologous groups. BLASTO incorporates the best-known multispecies ortholog databases, including NCBI Clusters of Orthologous Group, NCBI euKaryotic Orthologous Group database, OrthoMCL, MultiParanoid and TIGR Eukaryotic Gene Orthologues database, and offers a useful platform to integrate orthology information into functional inference and evolutionary studies of individual sequences. BLASTO is accessible online at http://oxytricha.princeton.edu/BlastO.
我们展示了直系同源组上的BLAST（BLASTO），这是一种经过改进的用于搜索直系同源组数据的BLAST工具。它将每个直系同源组视为一个单元，并输出直系同源组的排名列表，而不是单个序列。通过过滤冗余和假定的旁系同源物，与直系同源组而非数据库中的单个序列进行序列比较，可以改善功能预测和系统发育推断。BLASTO基于直系同源组中各个BLAST命中结果计算每个直系同源组的显著性得分，并将组中的分类单元数量用作可选权重。这允许用户控制直系同源组的物种多样性。BLASTO整合了最知名的多物种直系同源数据库，包括NCBI直系同源组簇、NCBI真核生物直系同源组数据库、OrthoMCL、MultiParanoid和TIGR真核生物基因直系同源物数据库，并提供了一个将直系同源信息整合到单个序列的功能推断和进化研究中的有用平台。可通过http://oxytricha.princeton.edu/BlastO在线访问BLASTO。
Zotero 插件