Striped Smith-Waterman speeds database searches six times over other SIMD implementations Export

@article{citeulike:1068475, abstract = {Motivation: The only algorithm guaranteed to find the optimal local alignment is the Smith-Waterman. It is also one of the slowest due to the number of computations required for the search. To speed up the algorithm, Single-Instruction Multiple-Data (SIMD) instructions have been used to parallelize the algorithm at the instruction level. Results: A faster implementation of the Smith-Waterman algorithm is presented. This algorithm achieved 2-8 times performance improvement over other SIMD based Smith-Waterman implementations. On a 2.0 GHz Xeon Core 2 Duo processor, speeds of >3.0 billion cell updates/s were achieved. Availability: http://farrar.michael.googlepages.com/Smith-waterman Contact: farrar.michael@gmail.com 10.1093/bioinformatics/btl582}, author = {Farrar, Michael}, citeulike-article-id = {1068475}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btl582}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/23/2/156.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/23/2/156.full.pdf}, citeulike-linkout-3 = {http://www.ingentaconnect.com/content/oup/cabios/2007/00000023/00000002/art00156}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/17110365}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=17110365}, day = {15}, doi = {10.1093/bioinformatics/btl582}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {computational\_biology, sequence\_alignment, simd, smith\_waterman}, month = {January}, number = {2}, pages = {156--161}, posted-at = {2009-11-10 23:26:31}, priority = {2}, publisher = {Oxford University Press}, title = {Striped Smith-Waterman speeds database searches six times over other SIMD implementations}, url = {http://dx.doi.org/10.1093/bioinformatics/btl582}, volume = {23}, year = {2007} }

TY - JOUR ID - citeulike:1068475 L3 - citeulike-article-id:1068475 N2 - Motivation: The only algorithm guaranteed to find the optimal local alignment is the Smith-Waterman. It is also one of the slowest due to the number of computations required for the search. To speed up the algorithm, Single-Instruction Multiple-Data (SIMD) instructions have been used to parallelize the algorithm at the instruction level. Results: A faster implementation of the Smith-Waterman algorithm is presented. This algorithm achieved 2-8 times performance improvement over other SIMD based Smith-Waterman implementations. On a 2.0 GHz Xeon Core 2 Duo processor, speeds of >3.0 billion cell updates/s were achieved. Availability: http://farrar.michael.googlepages.com/Smith-waterman Contact: farrar.michael@gmail.com 10.1093/bioinformatics/btl582 IS - 2 JF - Bioinformatics SN - 1367-4803 EP - 161 TI - Striped Smith-Waterman speeds database searches six times over other SIMD implementations PB - Oxford University Press VL - 23 SP - 156 KW - computational_biology KW - sequence_alignment KW - simd KW - smith_waterman AU - Farrar, Michael PY - 2007/01/15/ UR - http://dx.doi.org/10.1093/bioinformatics/btl582 ER -