A bit-string longest-common-subsequence algorithm
Information Processing Letters
Sparse dynamic programming I: linear cost functions
Journal of the ACM (JACM)
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Bounds for the String Editing Problem
Journal of the ACM (JACM)
A fast algorithm for computing longest common subsequences
Communications of the ACM
A linear space algorithm for computing maximal common subsequences
Communications of the ACM
A fast and practical bit-vector algorithm for the longest common subsequence problem
Information Processing Letters
A Survey of Longest Common Subsequence Algorithms
SPIRE '00 Proceedings of the Seventh International Symposium on String Processing Information Retrieval (SPIRE'00)
The constrained longest common subsequence problem
Information Processing Letters
A simple algorithm for the constrained sequence problems
Information Processing Letters
Cache-oblivious dynamic programming
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
Speeding up transposition-invariant string matching
Information Processing Letters
Algorithms on Strings
Proceedings of the 40th Conference on Winter Simulation
Transposition invariant string matching
Journal of Algorithms
Time and space efficient algorithms for constrained sequence alignment
CIAA'04 Proceedings of the 9th international conference on Implementation and Application of Automata
Partial duplicate detection for large book collections
Proceedings of the 20th ACM international conference on Information and knowledge management
Finding translations in scanned book collections
SIGIR '12 Proceedings of the 35th international ACM SIGIR conference on Research and development in information retrieval
Hi-index | 0.00 |
Modern graphical processing units (GPUs) offer much more computational power than modern central processing units. Therefore, it is natural that GPUs are applied not only for their original purposes, but also for general processing (GPGPU). In the field of sequence processing, one of the most important problems is the measuring of sequence similarity. There are many sequence similarity measures, e.g. edit distance, longest common subsequence length, and their derivatives. We examine the possibility of speeding up the algorithms computing some of them. We chose three measures useful in different situations. The experimental results show that the GPU versions of the examined algorithms are faster than their serial counterparts by a factor between 4 and 65. Copyright © 2010 John Wiley & Sons, Ltd.