Software—Practice & Experience
A very fast substring search algorithm
Communications of the ACM
A new approach to text searching
Communications of the ACM
Text algorithms
Experimental results on string matching algorithms
Software—Practice & Experience
String matching in the DNA alphabet
Software—Practice & Experience
A new string-pattern matching algorithm using partitioning and hashing efficiently
Journal of Experimental Algorithmics (JEA)
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)
A Bit-Parallel Approach to Suffix Automata: Fast Extended String Matching
CPM '98 Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching
Shift-or string matching with super-alphabets
Information Processing Letters
Efficient randomized pattern-matching algorithms
IBM Journal of Research and Development - Mathematics and computing
Multipattern string matching with q-grams
Journal of Experimental Algorithmics (JEA)
The wide window string matching algorithm
Theoretical Computer Science
Fast exact string matching algorithms
Information Processing Letters
The exact online string matching problem: A review of the most recent results
ACM Computing Surveys (CSUR)
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In this paper, we propose Genomic-oriented Rapid Algorithm for String Pattern-match (GRASPm), an algorithm centred on overlapped 2-grams analysis, which introduces a novel filtering heuristic – the compatibility rule – achieving significant efficiency gain. GRASPm's foundations rely especially on a wide searching window having the central duplet as reference for fast filtering of multiple alignments. Subsequently, superfluous detailed verifications are summarily avoided by filtering the incompatible alignments using the idcd (involving duplet of central duplet) concept combined with pre-processed conditions, allowing fast parallel testing for multiple alignments. Comparative performance analysis, using diverse genomic data, shows that GRASPm is faster than its competitors.