BACKGROUND:The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. RESULTS:We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. CONCLUSION:The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

译文

背景:功能性非编码RNA序列的发现已引起人们对与RNA分析相关的算法的日益增长的兴趣。但是,传统的序列比对算法无法计算出低同源性RNA序列的可靠比对。 RNA序列的空间构象在很大程度上决定了它们的功能,因此RNA比对算法必须考虑结构信息。
结果:我们提出了一种基于图的序列结构比对表示法,我们将其建模为整数线性程序(ILP)。我们概述了如何使用组合优化中的方法来计算ILP的最佳解决方案或接近最佳解决方案的方法,并在最近发布的RNA比对基准组上给出了结果。
结论:我们的算法的实现在两个已发布分数方面比我们测试的其他程序产生了更好的比对:在输入序列数量不断增加的情况下尤其如此。我们的程序LARA可从http://www.planet-lisa.net免费用于学术目的。

+1
+2
100研值 100研值 ¥99课程
检索文献一次
下载文献一次

去下载>

成功解锁2个技能,为你点赞

《SCI写作十大必备语法》
解决你的SCI语法难题!

技能熟练度+1

视频课《玩转文献检索》
让你成为检索达人!

恭喜完成新手挑战

手机微信扫一扫,添加好友领取

免费领《Endnote文献管理工具+教程》

微信扫码, 免费领取

手机登录

获取验证码
登录