Memory efficient folding algorithms for circular RNA secondary structures
Memory efficient folding algorithms for circular RNA secondary structures
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DOI：
10.1093/bioinformatics/btl023
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发表时间：
2006-05-15
期刊：
影响因子：
5.8
通讯作者：
Stadler, PF
中科院分区：
文献类型：
--
作者：
Hofacker, IL;Stadler, PF
背景：一小类RNA分子，特别是类病毒的微小基因组，是环状的。然而，大多数结构预测算法只处理线性RNA。最直接的方法是从由碱基对分开的“内部”和“外部”子结构计算圆形结构。这是不兼容的，但是，与内存节省的方法的维也纳RNA包，建立一个线性RNA结构从较短的（内部）structures.Result：在这里，我们描述了如何循环二级结构可以得到没有额外的内存要求作为一种“后处理”的线性结构。
Background: A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach is to compute circular structures from 'internal' and 'external' substructures separated by a base pair. This is incompatible, however, with the memory-saving approach of the Vienna RNA Package which builds a linear RNA structure from shorter (internal) structures only.Result: Here we describe how circular secondary structures can be obtained without additional memory requirements as a kind of 'post-processing' of the linear structures.