TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction
TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction
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DOI：
10.1093/molbev/msu117
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发表时间：
2014-06-01
影响因子：
10.7
通讯作者：
Notredame, Cedric
中科院分区：
文献类型：
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作者：
Chang, Jia-Ming;Di Tommaso, Paolo;Notredame, Cedric
多序列比对（MSA）是分析生物序列的关键建模过程。同源性和进化建模是MSA最常见的应用。众所周知，两者都对底层MSA的准确性敏感。在这项工作中，我们展示了如何使用传递一致性得分（TCS），T-咖啡评分方案的扩展版本，可以部分克服这个问题。使用这个本地的评价函数，我们表明，可以确定最可靠的部分MSA，从BAliBASE和PREFAB基于结构的参考比对判断。我们还展示了如何使用这一措施可以用来改善系统发育树重建既建立了模拟数据集和一个新的经验酵母数据集。出于这个目的，我们描述了一种新的无损替代网站过滤，涉及超重值得信赖的列。我们的方法依赖于T-Coffee框架;它使用成对比对库来评估任何第三方MSA。成对投影可以使用快速或慢速方法产生，从而允许在速度和精度之间进行权衡。我们将TCS与Heads-or-Tails，GUIDANCE，Gblocks和trimAl进行了比较，发现它可以显著提高结构准确性和更准确的系统发育树的估计。该软件可从www.tcoffee.org/Projects/tcs获得。
Multiple sequence alignment (MSA) is a key modeling procedure when analyzing biological sequences. Homology and evolutionary modeling are the most common applications of MSAs. Both are known to be sensitive to the underlying MSA accuracy. In this work, we show how this problem can be partly overcome using the transitive consistency score (TCS), an extended version of the T-Coffee scoring scheme. Using this local evaluation function, we show that one can identify the most reliable portions of an MSA, as judged from BAliBASE and PREFAB structure-based reference alignments. We also show how this measure can be used to improve phylogenetic tree reconstruction using both an established simulated data set and a novel empirical yeast data set. For this purpose, we describe a novel lossless alternative to site filtering that involves overweighting the trustworthy columns. Our approach relies on the T-Coffee framework; it uses libraries of pairwise alignments to evaluate any third party MSA. Pairwise projections can be produced using fast or slow methods, thus allowing a trade-off between speed and accuracy. We compared TCS with Heads-or-Tails, GUIDANCE, Gblocks, and trimAl and found it to lead to significantly better estimates of structural accuracy and more accurate phylogenetic trees. The software is available from www.tcoffee.org/Projects/tcs.