MAFFT-DASH: integrated protein sequence and structural alignment
MAFFT-DASH: integrated protein sequence and structural alignment
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DOI：
10.1093/nar/gkz342
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发表时间：
2019-07-02
影响因子：
14.9
通讯作者：
Katoh, Kazutaka
中科院分区：
文献类型：
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作者：
Rozewicki, John;Li, Songling;Katoh, Kazutaka
在这里，我们描述了一个Web服务器，它集成了MAFFT多序列比对（MSA）工具的结构比对。为此，我们准备了一个基于Web的对齐结构同源物数据库（DASH），它提供了蛋白质数据库（PDB）中所有蛋白质在结构域和链水平上的结构对齐，并且可以交互式查询或通过简单的REST类API查询。MAFFT-DASH集成可以在Web（https：//mafft.cbrc.jp/website/server/）或MAFFT的命令行版本上使用单个标志调用。在我们使用来自BAliBase，HomFam，OXFam，Mattbench和SISYPHUS数据集的878个案例的基准测试中，MAFFT-DASH在弱相似性的MSA问题上显示出10-20%的改进，就配对总和（SP）而言，这是一种衡量程序与参考比对相比在比对输入序列方面成功程度的指标。当用同源序列补充MAFFT比对时，观察到进一步的改善。MSA富集之外的DASH的潜在应用包括通过检测远程同源性的功能注释和用于同源性建模的模板文库的组装。
Here, we describe a web server that integrates structural alignments with the MAFFT multiple sequence alignment (MSA) tool. For this purpose, we have prepared a web-based Database of Aligned Structural Homologs (DASH), which provides structural alignments at the domain and chain levels for all proteins in the Protein Data Bank (PDB), and can be queried interactively or by a simple REST-like API. MAFFT-DASH integration can be invoked with a single flag on either the web (https://mafft.cbrc.jp/alignment/server/) or command-line versions of MAFFT. In our benchmarks using 878 cases from the BAliBase, HomFam, OXFam, Mattbench and SISYPHUS datasets, MAFFT-DASH showed 10-20% improvement over standard MAFFT for MSA problems with weak similarity, in terms of Sum-of-Pairs (SP), a measure of how well a program succeeds at aligning input sequences in comparison to a reference alignment. When MAFFT alignments were supplemented with homologous sequences, further improvement was observed. Potential applications of DASH beyond MSA enrichment include functional annotation through detection of remote homology and assembly of template libraries for homology modeling.