A new approach to text searching
SIGIR '89 Proceedings of the 12th annual international ACM SIGIR conference on Research and development in information retrieval
Fast text searching: allowing errors
Communications of the ACM
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
NR-grep: a fast and flexible pattern-matching tool
Software—Practice & Experience
Flexible pattern matching in strings: practical on-line search algorithms for texts and biological sequences
Computer Architecture, Fourth Edition: A Quantitative Approach
Computer Architecture, Fourth Edition: A Quantitative Approach
Proceedings of the 19th international conference on Parallel architectures and compilation techniques
Initial experiences porting a bioinformatics application to a graphics processor
PCI'05 Proceedings of the 10th Panhellenic conference on Advances in Informatics
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Text matching with errors is a regular task in computational biology. We present an extension of the bit-parallel Wu-Manber algorithm [16] to combine several searches for a pattern into a collection of fixed-length words. We further present an OpenCL parallelization of a redundant index on massively parallel multicore processors, within a framework of searching for similarities with seed-based heuristics. We successfully implemented and ran our algorithms on GPU and multicore CPU. Some speedups obtained are more than 60×.