一种基于自然数的线性时间滤波方法，用于发现DNA模式的所有出现

2006 Fourth International Conference on Intelligent Sensing and Information Processing Pub Date : 2006-12-01 DOI:10.1109/ICISIP.2006.4286078

V. Le

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引用次数: 2

摘要

字符串匹配和搜索技术在不同的研究工作中得到了广泛的研究。它们目前在计算生物学领域发挥着重要作用。这些技术中的大多数，从经典到改进版本，都可以在线性时间内成功地完成任务。在本文中，我提出了一种新的搜索方法，该方法基于在四个核苷酸的过渡矩阵上传递不同的自然数，以找到给定字符串中DNA模式的所有出现。在最坏的情况下，我的算法只有Theta(n - 1)的时间复杂度，其中n是给定字符串的长度s，对于长度为m的DNA模式p进行搜索。

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A natural number based linear time filtering approach to finding all occurrences of a DNA pattern

String matching and searching techniques have been extensively studied in different research works. They currently play an essential part in the field of computational biology. Most of those techniques, from classics to their improved versions could successfully accomplish the task in linear time. In this paper, I propose a new searching approach based on the delivery of distinct natural numbers over a transition matrix of four nucleotides to find all occurrences of a DNA pattern in a given string. My algorithm has only Theta(n - 1) time complexity for the worst case with n to be the length of a given string s for a DNA pattern p of length m to be searched on.

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2006 Fourth International Conference on Intelligent Sensing and Information Processing

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