By Topic

Highly scalable and accurate seeds for subsequence alignment

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$31 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

2 Author(s)
Pol, A. ; Dept. of Comput. & Information Sci. & Eng., Florida Univ., Gainesville, FL, USA ; Kahveci, T.

We propose a method for finding seeds for the local alignment of two nucleotide sequences. Our method uses randomized algorithms to find approximate seeds. We present a dynamic index to store the fingerprints of k-grams and a highly scalable and accurate (HSA) algorithm to incorporate randomization into process of seed generation. Experimental results show that our method produces better quality seeds with improved running time and memory usage compared to traditional non-spaced and spaced seeds. The presented algorithm scales very well with higher seed lengths while maintaining the quality and performance.

Published in:

Bioinformatics and Bioengineering, 2005. BIBE 2005. Fifth IEEE Symposium on

Date of Conference:

19-21 Oct. 2005