|
|
|
|
Searching DNA sequences based on similarity using designed spaced seed is shown in PatternHunter to be more sensitive and efficient than consecutive seed (as in BLAST). This makes spaced seed a better choice than conventional consecutive seed for hit scanning in a BLAST-like approach. Optimized multiple spaced seeds were proposed but they suffer from poor scalability requiring a separate table structure for every seed used and increases computational time with more table lookups. In this work, we study the design of multiple spaced seeds and proposed a novel approach that introduces gaps of various length into seeds. The gaps allow for variation in matching and thus increases the sensitivity. |
|
Send mail to
gunjanch@comp.nus.edu.sg with
questions or comments about this web site.
|
