全对全序列匹配的平均快速算法

6th International Symposium on String Processing and Information Retrieval. 5th International Workshop on Groupware (Cat. No.PR00268) Pub Date : 1999-09-21 DOI:10.1109/SPIRE.1999.796573

Ricardo Baeza-Yates, G. Gonnet

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引用次数: 38

摘要

我们提出了一种算法，该算法试图从基因序列数据库中对子序列进行对齐。该算法模拟了数据库后缀数组上的经典动态规划对齐算法。我们提供了一个详细的平均案例分析，表明该算法的运行时间相对于数据库大小是次二次的。一个类似的算法在亚线性平均时间内解决了近似字符串匹配问题。

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A fast algorithm on average for all-against-all sequence matching

We present an algorithm which attempts to align pairs of subsequences from a database of genetic sequences. The algorithm simulates the classical dynamic programming alignment algorithm over a suffix array of the database. We provide a detailed average case analysis which shows that the running time of the algorithm is subquadratic with respect to the database size. A similar algorithm solves the approximate string matching problem in sublinear average time.

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6th International Symposium on String Processing and Information Retrieval. 5th International Workshop on Groupware (Cat. No.PR00268)

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