Theoretical Computer Science
SIAM Journal on Computing
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
Approximate Boyer-Moore string matching
SIAM Journal on Computing
Fast string matching with mismatches
Information and Computation
Text algorithms
A comparison of approximate string matching algorithms
Software—Practice & Experience
A fast bit-vector algorithm for approximate string matching based on dynamic programming
Journal of the ACM (JACM)
Very fast and simple approximate string matching
Information Processing Letters
A fast string searching algorithm
Communications of the ACM
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
A guided tour to approximate string matching
ACM Computing Surveys (CSUR)
Text-Retrieval: Theory and Practice
Proceedings of the IFIP 12th World Computer Congress on Algorithms, Software, Architecture - Information Processing '92, Volume 1 - Volume I
Fast and Practical Approximate String Matching
CPM '92 Proceedings of the Third Annual Symposium on Combinatorial Pattern Matching
Boyer-Moore Strategy to Efficient Approximate String Matching
CPM '96 Proceedings of the 7th Annual Symposium on Combinatorial Pattern Matching
A Bit-Parallel Approach to Suffix Automata: Fast Extended String Matching
CPM '98 Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
A guided tour to approximate string matching
ACM Computing Surveys (CSUR)
Compact DFA Representation for Fast Regular Expression Search
WAE '01 Proceedings of the 5th International Workshop on Algorithm Engineering
String Matching with Stopper Encoding and Code Splitting
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
Faster Bit-Parallel Approximate String Matching
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
Regular expression searching on compressed text
Journal of Discrete Algorithms
Average-optimal single and multiple approximate string matching
Journal of Experimental Algorithmics (JEA)
LZgrep: a Boyer–Moore string matching tool for Ziv–Lempel compressed text: Research Articles
Software—Practice & Experience
Increased bit-parallelism for approximate and multiple string matching
Journal of Experimental Algorithmics (JEA)
Multipattern string matching with q-grams
Journal of Experimental Algorithmics (JEA)
The wide window string matching algorithm
Theoretical Computer Science
A programmable array processor architecture for flexible approximate string matching algorithms
Journal of Parallel and Distributed Computing
Fast exact string matching algorithms
Information Processing Letters
Extending q-grams to estimate selectivity of string matching with low edit distance
VLDB '07 Proceedings of the 33rd international conference on Very large data bases
Processor array architectures for flexible approximate string matching
Journal of Systems Architecture: the EUROMICRO Journal
Succinct backward-DAWG-matching
Journal of Experimental Algorithmics (JEA)
Approximate substring selectivity estimation
Proceedings of the 12th International Conference on Extending Database Technology: Advances in Database Technology
Multi-patterns parameterized shift-and string matching algorithm with super alphabets
Proceedings of the International Conference on Advances in Computing, Communication and Control
Simple Random Access Compression
Fundamenta Informaticae
Efficient Exact Pattern-Matching in Proteomic Sequences
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
A Bit-Parallel Exact String Matching Algorithm for Small Alphabet
FAW '09 Proceedings of the 3d International Workshop on Frontiers in Algorithmics
GRASPm: an efficient algorithm for exact pattern-matching in genomic sequences
International Journal of Bioinformatics Research and Applications
Average-optimal string matching
Journal of Discrete Algorithms
Improving practical exact string matching
Information Processing Letters
A fast bit-parallel multi-patterns string matching algorithm for biological sequences
ISB '10 Proceedings of the International Symposium on Biocomputing
Efficient bit-parallel multi-patterns string matching algorithms for limited expression
Proceedings of the Third Annual ACM Bangalore Conference
Tuning string matching for huge pattern sets
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Software maintenance by multi-patterns parameterized string matching with q-gram
ACM SIGSOFT Software Engineering Notes
Parameterized string matching: an application to software maintenance
ACM SIGSOFT Software Engineering Notes
Simple compression code supporting random access and fast string matching
WEA'07 Proceedings of the 6th international conference on Experimental algorithms
Algorithms for weighted matching
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
A new taxonomy of sublinear right-to-left scanning keyword pattern matching algorithms
Science of Computer Programming
Indexing methods for approximate dictionary searching: Comparative analysis
Journal of Experimental Algorithmics (JEA)
Special factors and the combinatorics of suffix and factor automata
Theoretical Computer Science
Efficient algorithm for detecting parameterized multiple clones in a large software system
ICCSA'11 Proceedings of the 2011 international conference on Computational science and Its applications - Volume Part V
Bit-parallel search algorithms for long patterns
SEA'10 Proceedings of the 9th international conference on Experimental Algorithms
Journal of Discrete Algorithms
On bit-parallel processing of multi-byte text
AIRS'04 Proceedings of the 2004 international conference on Asian Information Retrieval Technology
A compact representation of nondeterministic (suffix) automata for the bit-parallel approach
Information and Computation
From nondeterministic suffix automaton to lazy suffix tree
Algorithms and Applications
Practical and optimal string matching
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
Average complexity of backward q-gram string matching algorithms
Information Processing Letters
Simple Random Access Compression
Fundamenta Informaticae
Fast matching method for DNA sequences
ESCAPE'07 Proceedings of the First international conference on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies
Fast multiple string matching using streaming SIMD extensions technology
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
The exact online string matching problem: A review of the most recent results
ACM Computing Surveys (CSUR)
Improving regular-expression matching on strings using negative factors
Proceedings of the 2013 ACM SIGMOD International Conference on Management of Data
String matching with lookahead
Discrete Applied Mathematics
On a compact encoding of the swap automaton
Information Processing Letters
Hi-index | 0.00 |
The most important features of a string matching algorithm are its efficiency and its flexibility. Efficiency has traditionally received more attention, while flexibility in the search pattern is becoming a more and more important issue. Most classical string matching algorithms are aimed at quickly finding an exact pattern in a text, being Knuth-Morris-Pratt (KMP) and the Boyer-Moore (BM) family the most famous ones. A recent development uses deterministic "suffix automata" to design new optimal string matching algorithms, e.g. BDM and TurboBDM. Flexibility has been addressed quite separately by the use of "bit-parallelism", which simulates automata in their nondeterministic form by using bits and exploiting the intrinsic parallelism inside the computer word, e.g. the Shift-Or algorithm. Those algorithms are extended to handle classes of characters and errors in the pattern and/or in the text, their drawback being their inability to skip text characters. In this paper we merge bit-parallelism and suffix automata, so that a nondeterministic suffix automaton is simulated using bit-parallelism. The resulting algorithm, called BNDM, obtains the best from both worlds. It is much simpler to implement than BDM and nearly as simple as Shift-Or. It inherits from Shift-Or the ability to handle flexible patterns and from BDM the ability to skip characters. BNDM is 30%-40% faster than BDM and up to 7 times faster than Shift-Or. When compared to the fastest existing algorithms on exact patterns (which belong to the BM family), BNDM is from 20% slower to 3 times faster, depending on the alphabet size. With respect to flexible pattern searching, BNDM is by far the fastest technique to deal with classes of characters and is competitive to search allowing errors. In particular, BNDM seems very adequate for computational biology applications, since it is the fastest algorithm to search on DNA sequences and flexible searching is an important problem in that area. As a theoretical development related to flexible pattern matching, we introduce a new automaton to recognize suffixes of patterns with classes of characters. To the best of our knowledge, this automaton has not been studied before.