Fast computation of good multiple spaced seeds
(2007) 7th International Workshop on Algorithms in Bioinformatics (WABI 2007) 4645. p.346-358- Abstract
- Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. A significant fraction of computing power in the world is dedicated to performing such tasks. The introduction of optimal spaced seeds by Ma et al. has increased both the sensitivity and the speed of homology search and it has been adopted by many alignment programs such as BLAST. With the further improvement provided by multiple spaced seeds in PatternHunterII, the sensitivity of dynamic programming is approached at BLASTn speed. Whereas computing optimal multiple spaced seeds was proved to be NP-hard, we show that, from practical point of view, computing good ones can be very efficient. We give a simple heuristic algorithm which... (More)
- Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. A significant fraction of computing power in the world is dedicated to performing such tasks. The introduction of optimal spaced seeds by Ma et al. has increased both the sensitivity and the speed of homology search and it has been adopted by many alignment programs such as BLAST. With the further improvement provided by multiple spaced seeds in PatternHunterII, the sensitivity of dynamic programming is approached at BLASTn speed. Whereas computing optimal multiple spaced seeds was proved to be NP-hard, we show that, from practical point of view, computing good ones can be very efficient. We give a simple heuristic algorithm which computes good multiple seeds in polynomial time. Computing sensitivity is not required. When allowing the computation of the sensitivity for few seeds, we obtain better multiple seeds than previous ones in much shorter time. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/1409920
- author
- Ilie, Lucian and Ilie, Silvana LU
- organization
- publishing date
- 2007
- type
- Chapter in Book/Report/Conference proceeding
- publication status
- published
- subject
- keywords
- BLAST, PatternHunterII, string overlaps, sensitivity, homology search, multiple spaced seeds
- host publication
- Algorithms in Bioinformatics, Proceedings (Lecture Notes in Computer Science)
- volume
- 4645
- pages
- 346 - 358
- publisher
- Springer
- conference name
- 7th International Workshop on Algorithms in Bioinformatics (WABI 2007)
- conference location
- Philadelphia, Pennsylvania, United States
- conference dates
- 2007-09-08 - 2007-09-09
- external identifiers
-
- wos:000249739200031
- scopus:37249063588
- ISSN
- 1611-3349
- 0302-9743
- ISBN
- 978-3-540-74125-1
- DOI
- 10.1007/978-3-540-74126-8_32
- language
- English
- LU publication?
- yes
- additional info
- The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Numerical Analysis (011015004)
- id
- f15fdb87-833f-456e-a757-ce71a87c82a5 (old id 1409920)
- date added to LUP
- 2016-04-01 11:51:03
- date last changed
- 2024-01-07 22:52:55
@inproceedings{f15fdb87-833f-456e-a757-ce71a87c82a5, abstract = {{Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. A significant fraction of computing power in the world is dedicated to performing such tasks. The introduction of optimal spaced seeds by Ma et al. has increased both the sensitivity and the speed of homology search and it has been adopted by many alignment programs such as BLAST. With the further improvement provided by multiple spaced seeds in PatternHunterII, the sensitivity of dynamic programming is approached at BLASTn speed. Whereas computing optimal multiple spaced seeds was proved to be NP-hard, we show that, from practical point of view, computing good ones can be very efficient. We give a simple heuristic algorithm which computes good multiple seeds in polynomial time. Computing sensitivity is not required. When allowing the computation of the sensitivity for few seeds, we obtain better multiple seeds than previous ones in much shorter time.}}, author = {{Ilie, Lucian and Ilie, Silvana}}, booktitle = {{Algorithms in Bioinformatics, Proceedings (Lecture Notes in Computer Science)}}, isbn = {{978-3-540-74125-1}}, issn = {{1611-3349}}, keywords = {{BLAST; PatternHunterII; string overlaps; sensitivity; homology search; multiple spaced seeds}}, language = {{eng}}, pages = {{346--358}}, publisher = {{Springer}}, title = {{Fast computation of good multiple spaced seeds}}, url = {{http://dx.doi.org/10.1007/978-3-540-74126-8_32}}, doi = {{10.1007/978-3-540-74126-8_32}}, volume = {{4645}}, year = {{2007}}, }