Department of Computer Science, University of Leipzig, Leipzig, Germany.
Bioinformatics. 2011 Jan 15;27(2):279-80. doi: 10.1093/bioinformatics/btq642. Epub 2010 Nov 13.
Small nucleolar RNAs (snoRNAs) are an abundant class of non-coding RNAs with a wide variety of cellular functions including chemical modification of RNA, telomere maintanance, pre-rRNA processing and regulatory activities in alternative splicing. The main role of box C/D snoRNAs is to determine the targets for 2'-O-ribose methylation, which is important for rRNA maturation and splicing regulation of some mRNAs. The targets are still unknown, however, for many 'orphan' snoRNAs. While a fast and efficient target predictor for box H/ACA snoRNAs is available, no comparable tool exists for box C/D snoRNAs, even though they bind to their targets in a much less complex manner.
PLEXY is a dynamic programming algorithm that computes thermodynamically optimal interactions of a box C/D snoRNA with a putative target RNA. Implemented as scanner for large input sequences and equipped with filters on the duplex structure, PLEXY is an efficient and reliable tool for the prediction of box C/D snoRNA target sites.
The perl script PLEXY is freely available at http://www.bioinf.uni-leipzig.de/Software/PLEXY.
小核仁 RNA（snoRNA）是一类丰富的非编码 RNA，具有多种细胞功能，包括 RNA 的化学修饰、端粒维持、pre-rRNA 加工和可变剪接中的调节活性。框 C/D snoRNA 的主要作用是确定 2'-O-核糖甲基化的靶标，这对于 rRNA 成熟和一些 mRNA 的剪接调节很重要。然而，对于许多“孤儿” snoRNA 来说，其靶标仍然未知。虽然已经有一个快速有效的框 H/ACA snoRNA 靶标预测器，但对于框 C/D snoRNA 来说，仍然没有类似的工具，尽管它们与靶标结合的方式要简单得多。
PLEXY 是一种动态规划算法，用于计算框 C/D snoRNA 与假定靶 RNA 之间热力学最优的相互作用。作为大型输入序列的扫描仪实现，并配备了双链结构上的滤波器，PLEXY 是预测框 C/D snoRNA 靶位点的有效和可靠工具。
perl 脚本 PLEXY 可在 http://www.bioinf.uni-leipzig.de/Software/PLEXY 上免费获得。
