GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing
GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing
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DOI：
10.1093/bioinformatics/btk041
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发表时间：
2006-03-15
期刊：
影响因子：
5.8
通讯作者：
Giegerich, R
中科院分区：
文献类型：
--
作者：
Gerlach, W;Giegerich, R
动机：RNA二级结构分析通常需要在大的序列数据中寻找潜在的螺旋。结果：我们提出了一个实用程序GUUGle，它根据RNA碱基配对规则有效地定位潜在的螺旋区域，包括Watson-Crick和G-U对。它接受一组正序列和一组负序列，并根据RNA规则确定超过指定长度的正序列和负序列之间的所有精确匹配。GUUGle算法还可以适用于使用正序列集合的预计算后缀数组。我们展示了如何有效地将该程序用作计算成本更高的任务(如miRNA靶标预测)之前的过滤器。
Motivation: RNA secondary structure analysis often requires searching for potential helices in large sequence data.Results: We present a utility program GUUGle that efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a positive and a negative set of sequences, and determines all exact matches under RNA rules between positive and negative sequences that exceed a specified length. The GUUGle algorithm can also be adapted to use a precomputed suffix array of the positive sequence set. We show how this program can be effectively used as a filter preceding a more computationally expensive task such as miRNA target prediction.