Block edit models for approximate string matching
Theoretical Computer Science - Special issue: Latin American theoretical informatics
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
SIAM Journal on Discrete Mathematics
Approximate nearest neighbors and sequence comparison with block operations
STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing
Communication complexity of document exchange
SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
The string-to-string correction problem with block moves
ACM Transactions on Computer Systems (TOCS)
The string edit distance matching problem with moves
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
An Introduction to Data Structures and Algorithms
An Introduction to Data Structures and Algorithms
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Simple and Practical Sequence Nearest Neighbors with Block Operations
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes
CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
Efficient algorithms for the block edit problems
Information and Computation
Quick greedy computation for minimum common string partitions
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Scalable detection of frequent substrings by grammar-based compression
DS'11 Proceedings of the 14th international conference on Discovery science
Fast computation of a string duplication history under no-breakpoint-reuse
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
ESP-index: a compressed index based on edit-sensitive parsing
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
ESP-index: A compressed index based on edit-sensitive parsing
Journal of Discrete Algorithms
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The traditional edit-distance problem is to find the minimum number of insert-character and delete-character (and sometimes change character) operations required to transform one string into another. Here we consider the more general problem of a string represented by a singly linked list (one character per node) and being able to apply these operations to the pointer associated with a vertex as well as the character associated with the vertex. That is, in O(1) time, not only can characters be inserted or deleted, but substrings can be moved or deleted. We limit our attention to the ability to move substrings and leave substring deletions for future research. Note that O(1) time substring move operation implies O(1) substring exchange operation as well, a form of transformation that has been of interest in molecular biology. We show that this problem is NP-complete, and that a ''recursive'' sequence of moves can be simulated with at most a constant factor increase by a non-recursive sequence. Although a greedy algorithm is known to have poor (a polynomial factor) worst case performance, we present a polynomial time greedy algorithm for non-recursive moves which on a subclass of instances of a problem of size n achieves an approximation factor to optimal of at most O(logn). The development of this greedy algorithm shows how to reduce moves of substrings to moves of characters, and how to convert moves of characters to only inserts and deletes of characters.