Method and system for faster and more sensitive homology searching
US9652586B2 · kind B2 · utility
Assignee
Inventors
Key dates
| Filing date | Nov 17, 2006 |
| Grant date | May 16, 2017 |
| Priority date | — |
| Expiry date | May 14, 2030 |
Classification
- Technology area (CPC G)Physics
- CPC primaryG16B40/00
- WIPO fieldComputer technology
- WIPO sectorElectrical engineering
Abstract
An area of research in the field of bioinformatics deals with the identification of similarities within one, or between two DNA sequences. Current techniques are quite slow and many matches are missed. The invention provides a faster and more sensitive solution, by using “optimized spaced seeds” to perform these biological sequence homology searches. Various techniques are shown for identifying seeds which are optimized to improve the sensitivity or speed of the searching. In the preferred embodiment, optimized spaced seeds are determined by the parameters of the search and independent of the actual databases being searched (for example, using the length and weight of the spaced seed, as well as the probability of a hit in a similar region). Thus, these optimized seeds can be stored in libraries which are accessed as required.
Source: USPTO / EPO open patent data. Objective bibliographic and citation counts.