A very fast substring search algorithm
Communications of the ACM
A new approach to text searching
Communications of the ACM
Fast text searching: allowing errors
Communications of the ACM
A text compression scheme that allows fast searching directly in the compressed file
ACM Transactions on Information Systems (TOIS)
String matching in the DNA alphabet
Software—Practice & Experience
Let sleeping files lie: pattern matching in Z-compressed files
SODA '94 Proceedings of the fifth annual ACM-SIAM symposium on Discrete algorithms
A fast string searching algorithm
Communications of the ACM
Fast and flexible string matching by combining bit-parallelism and suffix automata
Journal of Experimental Algorithmics (JEA)
Flexible pattern matching in strings: practical on-line search algorithms for texts and biological sequences
A String Matching Algorithm Fast on the Average
Proceedings of the 6th Colloquium, on Automata, Languages and Programming
A Boyer-Moore Type Algorithm for Compressed Pattern Matching
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
Efficient Experimental String Matching by Weak Factor Recognition
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
A Very Fast String Matching Algorithm for Small Alphabeths and Long Patterns (Extended Abstract)
CPM '98 Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching
Speeding Up Pattern Matching by Text Compression
CIAC '00 Proceedings of the 4th Italian Conference on Algorithms and Complexity
Shift-or string matching with super-alphabets
Information Processing Letters
Compressed Pattern Matching in DNA Sequences
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
LZgrep: a Boyer–Moore string matching tool for Ziv–Lempel compressed text: Research Articles
Software—Practice & Experience
A simple fast hybrid pattern-matching algorithm
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Practical and optimal string matching
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
An Efficient Matching Algorithm for Encoded DNA Sequences and Binary Strings
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
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DNA sequences are the fundamental information for each species and a comparison between DNA sequences of different species is an important task. Since DNA sequences are very long and there exist many species, not only fast matching but also efficient storage is an important factor for DNA sequences. Thus, a fast string matching method suitable for encoded DNA sequences is needed. In this paper, we present a fast string matching method for encoded DNA sequences which does not decode DNA sequences while matching. We use four-characters-to-one-byte encoding and combine a suffix approach and a multipattern matching approach. Experimental results show that our method is about 5 times faster than AGREP and the fastest among known algorithms.