Detecting distant homology with Meta-BASIC
Detecting distant homology with Meta-BASIC
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DOI：
10.1093/nar/gkh370
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Rychlewski, L
中科院分区：
文献类型：
--
作者：
Ginalski, K;von Grotthuss, M;Rychlewski, L
Meta-BASIC (http://basic.bioinfo.pl) 是一种新颖的灵敏方法，用于基于元图谱的一致比对来识别蛋白质之间的远距离相似性。具体来说，Meta-BASIC 通过利用多种评分系统和比对算法来比较序列图谱与预测的二级结构。在我们的基准测试中，Meta-BASIC 的性能优于许多单独的服务器，包括折叠识别服务器，并且它可以与基于模型结构比较的元预测器竞争。此外，Meta-BASIC 具有高通量能力，即使参考蛋白的三级结构未知，也能够检测非常远的关系。这种新方法适用于 860 个功能未知 (DUF) 的 PfamA 蛋白家族，并提供了许多新颖的结构功能分配，可在线获取 http://basic.bioinfo.pl/duf.pl。对两个最有趣的作业进行了详细讨论。 DUF271 和 DUF431 预计分别是核苷酸二磷酸糖转移酶和 α/β 结 SAM 依赖性 RNA 甲基转移酶。
Meta-BASIC (http://basic.bioinfo.pl) is a novel sensitive approach for recognition of distant similarity between proteins based on consensus alignments of meta profiles. Specifically, Meta-BASIC compares sequence profiles combined with predicted secondary structure by utilizing several scoring systems and alignment algorithms. In our benchmarking tests, Meta-BASIC outperforms many individual servers, including fold recognition servers, and it can compete with meta predictors that base their strength on the structural comparison of models. In addition, Meta-BASIC, which enables detection of very distant relationships even if the tertiary structure for the reference protein is not known, has a high-throughput capability. This new method is applied to 860 PfamA protein families with unknown function (DUF) and provides many novel structure-functional assignments available on-line at http://basic.bioinfo.pl/duf.pl. Detailed discussion is provided for two of the most interesting assignments. DUF271 and DUF431 are predicted to be a nucleotide-diphospho-sugar transferase and an alpha/beta-knot SAM-dependent RNA methyltransferase, respectively.