Torarinsson Elfar, Havgaard Jakob H, Gorodkin Jan
Division of Genetics and Bioinformatics, IBHV and Center for Bioinformatics, University of Copenhagen, Frederiksberg C, Denmark.
Bioinformatics. 2007 Apr 15;23(8):926-32. doi: 10.1093/bioinformatics/btm049. Epub 2007 Feb 25.
An apparent paradox in computational RNA structure prediction is that many methods, in advance, require a multiple alignment of a set of related sequences, when searching for a common structure between them. However, such a multiple alignment is hard to obtain even for few sequences with low sequence similarity without simultaneously folding and aligning them. Furthermore, it is of interest to conduct a multiple alignment of RNA sequence candidates found from searching as few as two genomic sequences.
Here, based on the PMcomp program, we present a global multiple alignment program, foldalignM, which performs especially well on few sequences with low sequence similarity, and is comparable in performance with state of the art programs in general. In addition, it can cluster sequences based on sequence and structure similarity and output a multiple alignment for each cluster. Furthermore, preliminary results with local datasets indicate that the program is useful for post processing foldalign pairwise scans.
The program foldalignM is implemented in JAVA and is, along with some accompanying PERL scripts, available at http://foldalign.ku.dk/
计算RNA结构预测中一个明显的矛盾之处在于，许多方法在寻找一组相关序列之间的共同结构时，预先需要这些序列的多序列比对。然而，即使对于少数序列相似性较低的序列，在不同时进行折叠和比对的情况下，也很难获得这样的多序列比对。此外，对从搜索少至两个基因组序列中找到的RNA序列候选物进行多序列比对也很有意义。
在此，基于PMcomp程序，我们提出了一个全局多序列比对程序foldalignM，它在少数序列相似性较低的序列上表现特别出色，总体性能与现有最佳程序相当。此外，它可以根据序列和结构相似性对序列进行聚类，并为每个聚类输出一个多序列比对。此外，局部数据集的初步结果表明，该程序对于foldalign成对扫描的后处理很有用。
foldalignM程序用JAVA实现，可与一些附带的PERL脚本一起从http://foldalign.ku.dk/获取。
