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RNA结构预测工具PPfold 3.0
熊荣川 译
六盘水师范学院生物信息学实验室
http://blog.sciencenet.cn/u/Bearjazz
随着物理方法测定的 RNA结构数据越来越丰富,以及 RNA初级、高级结构之间关系研究的深入,现在涌现出一大批基于系统发生和已有 RNA结构数据库来预测未知 RNA结构的生物信息学方法,相应也产生了学多软件工具,下面简单的介绍其中一款软件PPfold 3.0。
PPfold 3.0一款基于Pfold算法的RNA二级结构预测工具软件,是PPfold的升级,更丰富了既有RNA结构的参考和算法的优化。该软件为java程序,不依赖任何操作系统,可以到以下地址下载安装使用。
http://birc.au.dk/software/ppfold.
原文:
PPfold 3.0: Fast RNA secondary structure prediction
using phylogeny and auxiliary data
Zsuzsanna S¨uk¨osd 1;2;3_, Bjarne Knudsen 4, Jørgen Kjems 1;2, and Christian
NS Pedersen 3;5
ABSTRACT PPfold is a multithreaded implementation of the Pfold algorithm for RNA secondary structure prediction. Here we present a new version of PPfold, which extends the evolutionary analysis with a
exible probabilistic model for incorporating auxiliary data, such as data from structure probing experiments. Our tests show that the accuracy of single-sequence secondary structure prediction using experimental data in PPfold 3.0 is comparable to RNAstructure. Furthermore, alignment structure prediction quality is improved even further by the addition of experimental data. PPfold 3.0 therefore has the potential of producing more accurate predictions than it was previously possible. Availability and Implementation PPfold 3.0 is available as a platform-independent Java application, and can be downloaded from http://birc.au.dk/software/ppfold.Contact Zsuzsanna S¨uk¨osd, zs@birc.au.dk.
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