Evaluating DNA sequence searching algorithms on multicore
by Ning Weng, Benfano Soewito
International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 1, No. 3, 2008

Abstract: Sequence searching is one of major operations in modern bioengineering. Recent emerging multicore provides a promising technology to enhance sequence searching performance. However, efficiently employing the multicore for a uniprocessor-oriented algorithm is a difficult task. This paper presents a methodology to profile processing requirements for DNA sequence search algorithms, parallelise them onto multicore, and analytically evaluate their performance. The key feature of this methodology is that entire processes are automated and it requires users little understanding of the complexity of algorithms and multicore hardware architecture. Our methodology considers three approaches to parallelise searching operations: queries, database, and task segmentation.

Online publication date: Wed, 26-Nov-2008

The full text of this article is only available to individual subscribers or to users at subscribing institutions.

 
Existing subscribers:
Go to Inderscience Online Journals to access the Full Text of this article.

Pay per view:
If you are not a subscriber and you just want to read the full contents of this article, buy online access here.

Complimentary Subscribers, Editors or Members of the Editorial Board of the International Journal of Computational Biology and Drug Design (IJCBDD):
Login with your Inderscience username and password:

    Username:        Password:         

Forgotten your password?


Want to subscribe?
A subscription gives you complete access to all articles in the current issue, as well as to all articles in the previous three years (where applicable). See our Orders page to subscribe.

If you still need assistance, please email subs@inderscience.com