Bit-Parallel Algorithm for the Block Variant of the Merged Longest Common Subsequence Problem

被引：2

作者：

Danek, Agnieszka ^{[1
]}

Deorowicz, Sebastian ^{[1
]}

机构：

[1] Silesian Tech Univ, Inst Informat, PL-44100 Gliwice, Poland

来源：

MAN-MACHINE INTERACTIONS 3 | 2014年 / 242卷

关键词：

sequence comparison; genome; longest common subsequence;

D O I：

10.1007/978-3-319-02309-0_18

中图分类号：

TP18 [人工智能理论];

学科分类号：

081104 ; 0812 ; 0835 ; 1405 ;

摘要：

The problem of comparison of genomic sequences is of great importance. There are various measures of similarity of sequences. One of the most popular is the length of the longest common subsequence (LCS). We propose the first bit-parallel algorithm for the variant of the LCS problem, block merged LCS, which was recently formulated in the studies on the whole genome duplication hypothesis. Practical experiments show that our proposal is from 10 to over 100 times faster than existing algorithms.

引用

页码：173 / 181

页数：9

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