The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification
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DOI：
10.1093/nar/gkt399
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发表时间：
2013-07-01
影响因子：
14.9
通讯作者：
Sjoelander, Kimmen
中科院分区：
文献类型：
--
作者：
Afrasiabi, Cyrus;Samad, Bushra;Sjoelander, Kimmen
PhyloFacts“快速近似树分类”（FAT-CAT）网络服务器提供了一种新的直系同源识别方法，该方法使用基于子树隐藏马尔可夫模型的蛋白质序列放置到 PhyloFacts 数据库中的系统发育基因组直系同源组。微生物、植物和动物蛋白质数据集的结果表明，FAT-CAT 在分离直向同源物和旁系同源物方面具有高精度，并且对混杂结构域具有鲁棒性。我们还提出了记录基于子树隐马尔可夫模型评分的直系同源识别精度的结果。 FAT-CAT 系统发育放置用于导出查询的功能注释，包括置信度得分和向下钻取功能。 PhyloFacts 广泛的分类学和功能覆盖范围，包含来自整个生命树的超过 730 万种蛋白质，使 FAT-CAT 能够预测直系同源物并为大多数序列输入分配功能。提供四种管道参数预设来处理不同的序列类型，包括部分序列和含有混杂结构域的蛋白质；用户还可以修改个别参数。可以使用 PhyloScope Javascript 树查看器以交互方式在线查看与查询匹配的 PhyloFacts 树，并且超链接到各种外部数据库。 FAT-CAT Web 服务器位于 http://phylogenomics.berkeley.edu/phylofacts/fatcat/。
The PhyloFacts 'Fast Approximate Tree Classification' (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT's high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts' broad taxonomic and functional coverage, with >7.3M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyper-linked to various external databases. The FAT-CAT web server is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/.