An Efficient Matching Algorithm for Encoded DNA Sequences and Binary Strings

被引：0

作者：

Faro, Simone ^{[1
]}

Lecroq, Thierry ^{[2
]}

机构：

[1] Univ Catania, Dipartimento Matemat & Informat, I-95124 Catania, Italy

[2] Univ Rouen, LITIS EA 4108, F-76821 Mont St Aignan, France

来源：

COMBINATORIAL PATTERN MATCHING, PROCEEDINGS | 2009年 / 5577卷

关键词：

string matching; binary strings; DNA sequences; experimental algorithms; compressed text processing;

D O I：

暂无

中图分类号：

TP [自动化技术、计算机技术];

学科分类号：

0812 ;

摘要：

We present a new efficient algorithm for exact matching in encoded DNA sequences and on binary strings. Our algorithm combines a multi-pattern version of the BNDM algorithm and a simplified version of the COMMENTZ-WALTER algorithm. We performed also experimental comparisons with the most efficient algorithms presented in the literature. Experimental results show that the newly presented algorithm outperforms existing solutions in most cases.

引用

页码：106 / +

页数：2

共 50 条

[21] An Efficient Mining Algorithm for Key Segment from DNA Sequences
Mao, Guojun
2015 IEEE 28TH CANADIAN CONFERENCE ON ELECTRICAL AND COMPUTER ENGINEERING (CCECE), 2015, : 396 - 399
[22] A partition-based efficient algorithm for large scale mul tiple-strings matching
Liu, Ping
Liu, Yan-Bing
Tan, Jian-Long
String Processing and Information Retrieval, Proceedings, 2005, 3772 : 399 - 404
[23] An efficient algorithm for the identification of structured motifs in DNA promoter sequences
Carvalho, AM
Freitas, AT
Oliveira, AL
Sagot, MF
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2006, 3 (02) : 126 - 140
[24] The WM-q multiple exact string matching algorithm for DNA sequences
Karcioglu, Abdullah Ammar
Bulut, Hasan
COMPUTERS IN BIOLOGY AND MEDICINE, 2021, 136
[25] The WM-q multiple exact string matching algorithm for DNA sequences
Karcioglu, Abdullah Ammar
Bulut, Hasan
Computers in Biology and Medicine, 2021, 136
[26] Fast bitwise pattern-matching algorithm for DNA sequences on modern hardware
Ozcan, Giyasettin
Unsal, Osman Sabri
TURKISH JOURNAL OF ELECTRICAL ENGINEERING AND COMPUTER SCIENCES, 2015, 23 (05) : 1405 - 1417
[27] MEMORIZING BINARY VECTOR SEQUENCES BY A SPARSELY ENCODED NETWORK
BARAM, Y
IEEE TRANSACTIONS ON NEURAL NETWORKS, 1994, 5 (06): : 974 - 981
[28] The asymptotic induced matching number of hypergraphs: balanced binary strings
Arunachalam, Srinivasan
Vrana, Peter
Zuiddam, Jeroen
ELECTRONIC JOURNAL OF COMBINATORICS, 2020, 27 (03): : 1 - 30
[29] DE BRUIJN SEQUENCES FOR FIXED-WEIGHT BINARY STRINGS
Ruskey, Frank
Sawada, Joe
Williams, Aaron
SIAM JOURNAL ON DISCRETE MATHEMATICS, 2012, 26 (02) : 605 - 617
[30] AN ALGORITHM FOR MATCHING RUN-LENGTH CODED STRINGS
BUNKE, H
CSIRIK, J
COMPUTING, 1993, 50 (04) : 297 - 314

← 1 2 3 4 5 →