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13th IEEE International Conference on BioInformatics and BioEngineering (2005)
Minneapolis, Minnesota
Oct. 19, 2005 to Oct. 21, 2005
ISBN: 0-7695-2476-1
pp: 27-31
Abhijit Pol , University of Florida
Tamer Kahveci , University of Florida
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.

A. Pol and T. Kahveci, "Highly Scalable and Accurate Seeds for Subsequence Alignment," 13th IEEE International Conference on BioInformatics and BioEngineering(BIBE), Minneapolis, Minnesota, 2005, pp. 27-31.
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