FAST FOLDING AND COMPARISON OF RNA SECONDARY STRUCTURES
FAST FOLDING AND COMPARISON OF RNA SECONDARY STRUCTURES
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DOI：
10.1007/bf00818163
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发表时间：
1994-02-01
影响因子：
1.8
通讯作者：
SCHUSTER, P
中科院分区：
文献类型：
--
作者：
HOFACKER, IL;FONTANA, W;SCHUSTER, P
提出了基于动态编程算法的计算计算和比较RNA二级结构，维也纳RNA包装的代码，旨在预测具有最低自由能的结构以及平衡分区功能和基础配对概率的计算引入了RNA的反折叠问题的有效启发式。此外，我们提出了基于树编辑和对齐的RNA二级结构进行比较的紧凑，有效的程序。所有计算机代码均以ANSI C编写。它们包括在具有分布式内存的并行计算机上修改算法的实现。在Intel HyperCube上进行的性能分析表明，序列的时间越长，并行计算逐渐变得越来越有效。
Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.