基于多序列比对的RNA-RNA相互作用预测
RNA-RNA interaction prediction based on multiple sequence alignments
摘要：
目前已经发展了许多计算机化的RNA-RNA相互作用结构预测方法。最近，$O(N^6)$时间和$O(N^4)$空间动态规划算法已经变得可用，其计算RNA-RNA相互作用复合物的配分函数。然而，这些方法很少结合相关序列的知识，因此相关的进化信息往往被忽略的结构确定。因此，引入一种同时考虑热力学稳定性和序列协变的方法具有相当大的实际意义。我们提出了\emph{a priori}折叠算法\texttt{ripalign}，其输入由两个（给定）多序列比对（MSA）。\texttt{ripalign}输出（1）配分函数，（2）碱基配对概率，（3）混合概率和（4）一组Boltzmann采样的次优结构，其由与比对兼容的规范联合结构组成。与单序列对折叠算法\texttt{rip}相比，\texttt{ripalign}所需的额外内存资源可以忽略不计。此外，我们将可能的结构约束作为输入参数到我们的算法。这里描述的算法是作为\texttt{rip}包的一部分用C实现的。补充材料、源代码和输入/输出文件可从\url{http://www.combinatorics.cn/cbpc/ripalign.html}免费下载。Christian Reidys \texttt{duck@santafe.edu}
英文摘要：
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes. However, few of these methods incorporate the knowledge concerning related sequences, thus relevant evolutionary information is often neglected from the structure determination. Therefore, it is of considerable practical interest to introduce a method taking into consideration both thermodynamic stability and sequence covariation. We present the \emph{a priori} folding algorithm \texttt{ripalign}, whose input consists of two (given) multiple sequence alignments (MSA). \texttt{ripalign} outputs (1) the partition function, (2) base-pairing probabilities, (3) hybrid probabilities and (4) a set of Boltzmann-sampled suboptimal structures consisting of canonical joint structures that are compatible to the alignments. Compared to the single sequence-pair folding algorithm \texttt{rip}, \texttt{ripalign} requires negligible additional memory resource. Furthermore, we incorporate possible structure constraints as input parameters into our algorithm. The algorithm described here is implemented in C as part of the \texttt{rip} package. The supplemental material, source code and input/output files can freely be downloaded from \url{http://www.combinatorics.cn/cbpc/ripalign.html}. \section{Contact} Christian Reidys \texttt{duck@santafe.edu}
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
