Striped Smith-Waterman speeds database searches six times over other SIMD implementations.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 17110365.
- No licence information is recorded for this record.
- Because redistribution is not established, this page shows the abstract only. Follow the links below for the full text.
Abstract
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. 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. http://farrar.michael.googlepages.com/Smith-waterman
Medical subject headings
- Algorithms
- Database Management Systems
- Databases, Genetic
- Information Storage and Retrieval
- Sequence Alignment
- Sequence Analysis