Parallel local sequence alignment
US9384239B2 · kind B2 · utility
Assignee
Inventors
Key dates
| Filing date | Dec 17, 2012 |
| Grant date | Jul 5, 2016 |
| Priority date | — |
| Expiry date | May 22, 2034 |
Classification
- Technology area (CPC G)Physics
- CPC primaryG16B30/10
- WIPO fieldComputer technology
- WIPO sectorElectrical engineering
Abstract
Various technologies described herein pertain to parallel local sequence alignment that aligns a query sequence with a database sequence. The database sequence is segmented into a plurality of stripes. A first processing unit can compute Smith-Waterman values for a first stripe of the database sequence across the query sequence based on a cost function that models biological similarity between sequences. Moreover, a second processing unit can compute Smith-Waterman values for a second stripe of the database sequence across the query sequence based on the cost function. Further, a subset of the Smith-Waterman values for the second stripe of the database sequence across the query sequence can be re-computed based on the cost function (e.g., by the first processing unit or the second processing unit). The subset of the Smith-Waterman values to be re-computed can be determined based on a query sequence length and the cost function.
Source: USPTO / EPO open patent data. Objective bibliographic and citation counts.