Hertel Jana, Stadler Peter F
Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
Bioinformatics. 2006 Jul 15;22(14):e197-202. doi: 10.1093/bioinformatics/btl257.
Recently, genome-wide surveys for non-coding RNAs have provided evidence for tens of thousands of previously undescribed evolutionary conserved RNAs with distinctive secondary structures. The annotation of these putative ncRNAs, however, remains a difficult problem. Here we describe an SVM-based approach that, in conjunction with a non-stringent filter for consensus secondary structures, is capable of efficiently recognizing microRNA precursors in multiple sequence alignments. The software was applied to recent genome-wide RNAz surveys of mammals, urochordates, and nematodes.
The program RNAmicro is available as source code and can be downloaded from http://www.bioinf.uni-leipzig/Software/RNAmicro.
最近，针对非编码RNA的全基因组调查为成千上万种以前未描述的具有独特二级结构的进化保守RNA提供了证据。然而，对这些假定的非编码RNA进行注释仍然是一个难题。在此，我们描述了一种基于支持向量机的方法，该方法结合了对共有二级结构的宽松筛选，能够在多序列比对中有效识别微小RNA前体。该软件已应用于最近对哺乳动物、尾索动物和线虫的全基因组RNAz调查。
程序RNAmicro以源代码形式提供，可从http://www.bioinf.uni-leipzig/Software/RNAmicro下载。
