R-Coffee: a method for multiple alignment of non-coding RNA
R-Coffee: a method for multiple alignment of non-coding RNA
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DOI：
10.1093/nar/gkn174
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发表时间：
2008-05-01
影响因子：
14.9
通讯作者：
Notredame, Cedric
中科院分区：
文献类型：
--
作者：
Wilm, Andreas;Higgins, Desmond G.;Notredame, Cedric
R-Coffee是一个多RNA比对软件包，源自T-Coffee，旨在比对RNA序列，同时利用二级结构信息。R-Coffee使用了一种将二级结构信息纳入比对中的重复评分方案。它作为比对改进剂特别有效，并且可以与任何现有的序列比对方法相结合。在这项工作中，我们使用R-Coffee来计算多个序列比对，结合序列比对器和结构比对器的成对输出。我们表明，R-Coffee可以提高所有序列比对的准确性。我们还表明，T-Coffee的基于一致性的组件可以提高几种结构比对的准确性。R-Coffee在388个BRAliBase参考数据集和11个更长的Cmfinder数据集上进行了测试。总之，我们的研究结果表明，最好的协议比对短序列（小于200 nt）是R-Coffee与RNA成对结构比对康桑的组合。我们还表明，四个最好的序列比对程序与R-Coffee的同时组合产生的比对几乎与R-Coffee/Consan获得的比对一样准确。最后，我们证明了R-Coffee也可以用于比对超出结构比对器通常范围的较长数据集。R-Coffee可从T-Coffee网站（www.tcoffee.org）免费下载，沿着文档。
R-Coffee is a multiple RNA alignment package, derived from T-Coffee, designed to align RNA sequences while exploiting secondary structure information. R-Coffee uses an alignment-scoring scheme that incorporates secondary structure information within the alignment. It works particularly well as an alignment improver and can be combined with any existing sequence alignment method. In this work, we used R-Coffee to compute multiple sequence alignments combining the pairwise output of sequence aligners and structural aligners. We show that R-Coffee can improve the accuracy of all the sequence aligners. We also show that the consistency-based component of T-Coffee can improve the accuracy of several structural aligners. R-Coffee was tested on 388 BRAliBase reference datasets and on 11 longer Cmfinder datasets. Altogether our results suggest that the best protocol for aligning short sequences (less than 200 nt) is the combination of R-Coffee with the RNA pairwise structural aligner Consan. We also show that the simultaneous combination of the four best sequence alignment programs with R-Coffee produces alignments almost as accurate as those obtained with R-Coffee/Consan. Finally, we show that R-Coffee can also be used to align longer datasets beyond the usual scope of structural aligners. R-Coffee is freely available for download, along with documentation, from the T-Coffee web site (www.tcoffee.org).