A novel approach to the detection of genomic approximate tandem repeats in the levenshtein metric
A novel approach to the detection of genomic approximate tandem repeats in the levenshtein metric
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DOI：
10.1089/cmb.2007.0018
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发表时间：
2007-09-01
影响因子：
1.7
通讯作者：
Preparata, Franco P.
中科院分区：
文献类型：
--
作者：
Domanic, Nevzat Onur;Preparata, Franco P.
提出了一种检测基因组序列中近似串联重复序列的有效算法。该算法基于创新的统计标准来检测可能包括串联重复序列的候选区域；随后通过基于动态规划的比对来验证这些区域。不需要关于周期大小或模式的事先信息。此外，该算法实际上能够检测任意周期的重复。算法的实现与两种最先进的串联重复检测工具进行了比较，以验证其在自然数据和合成数据上的有效性。该算法可在www.cs.brown.edu/People/Domanic/tandem/上找到。
An efficient algorithm for detecting approximate tandem repeats in genomic sequences is presented. The algorithm is based on innovative statistical criteria to detect candidate regions which may include tandem repeats; these regions are subsequently verified by alignments based on dynamic programming. No prior information about the period size or pattern is needed. Also, the algorithm is virtually capable of detecting repeats with any period. An implementation of the algorithm is compared with the two state-of-the-art tandem repeats detection tools to demonstrate its effectiveness both on natural and synthetic data. The algorithm is available at www.cs.brown.edu/people/domanic/tandem/.