Faster algorithms for string matching with k mismatches

Overlap matching

SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms

Approximate subset matching with Don't Cares

SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms

The string edit distance matching problem with moves

SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms

Overlap matching

Information and Computation

High Similarity Sequence Comparison in Clustering Large Sequence Databases

CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics

Computing Highly Specific and Mismatch Tolerant Oligomers Efficiently

CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics

Dictionary matching and indexing with errors and don't cares

STOC '04 Proceedings of the thirty-sixth annual ACM symposium on Theory of computing

An efficient DNA sequence searching method using position specific weighting scheme

Journal of Information Science

Approximate string matching using compressed suffix arrays

Theoretical Computer Science

The string edit distance matching problem with moves

ACM Transactions on Algorithms (TALG)

Bit-parallel string matching under Hamming distance in O(n⌈m/w⌉) worst case time

Information Processing Letters

Note: Pattern matching with pair correlation distance

Theoretical Computer Science

Pattern Matching with Pair Correlation Distance

SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval

Faster pattern matching with character classes using prime number encoding

Journal of Computer and System Sciences

Average-optimal string matching

Journal of Discrete Algorithms

An efficient algorithm for finding similar short substrings from large scale string data

PAKDD'08 Proceedings of the 12th Pacific-Asia conference on Advances in knowledge discovery and data mining

Pseudo-realtime pattern matching: closing the gap

CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching

Finding optimal alignment and consensus of circular strings

CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching

Periodicity in streams

APPROX/RANDOM'10 Proceedings of the 13th international conference on Approximation, and 14 the International conference on Randomization, and combinatorial optimization: algorithms and techniques

Pattern matching in the Hamming distance with thresholds

Information Processing Letters

Optimal spaced seeds for faster approximate string matching

ICALP'05 Proceedings of the 32nd international conference on Automata, Languages and Programming

A multi-level framework for the analysis of sequential data

Data Mining

Finding patterns with variable length gaps or don’t cares

COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics

Parallel pattern matching with swaps on a linear array

ICA3PP'10 Proceedings of the 10th international conference on Algorithms and Architectures for Parallel Processing - Volume Part I

String indexing for patterns with wildcards

SWAT'12 Proceedings of the 13th Scandinavian conference on Algorithm Theory

Exploiting word-level parallelism for fast convolutions and their applications in approximate string matching

European Journal of Combinatorics

Approximate regular expression matching with multi-strings

Journal of Discrete Algorithms

Sequential pattern mining -- approaches and algorithms

ACM Computing Surveys (CSUR)

PMBC: Pattern mining from biological sequences with wildcard constraints

Computers in Biology and Medicine