Analysis of Spaced Seed Technique in Sequence Alignment

Choi, Kwok-Pui; Zhang, Louxin

doi:10.1142/s0219607705000048

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COSMOS

2005

DOI: 10.1142/s0219607705000048

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Analysis of Spaced Seed Technique in Sequence Alignment

Kwok-Pui Choi

Louxin Zhang

Abstract: The novel introduction of spaced seed idea in the filtration step of sequence comparison by Ma, Tromp and Li (2002) has greatly increased the sensitivity of homology search without compromising the speed of search. In this paper, we survey some recent works on spaced seeds with main emphasis on their probabilistic and computational aspects.

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2007

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Cited by 1 publication

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Superiority of Spaced Seeds for Homology Search

Zhang

2007

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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In homology search, good spaced seeds have higher sensitivity for the same cost (weight). However, elucidating the mechanism that confers power to spaced seeds and characterizing optimal spaced seeds still remain unsolved. This paper investigates these two important open questions by formally analyzing the average number of non-overlapping hits and the hit probability of a spaced seed in the Bernoulli sequence model. We prove that when the length of a non-uniformly spaced seed is bounded above by an exponential function of the seed weight, the seed outperforms strictly the traditional consecutive seed of the same weight in both 1) the average number of non-overlapping hits and 2) the asymptotic hit probability. This clearly answers the first problem mentioned above in the Bernoulli sequence model. The theoretical study in this paper also gives a new solution to finding long optimal seeds.

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Superiority of Spaced Seeds for Homology Search

Zhang

2007

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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Analysis of Spaced Seed Technique in Sequence Alignment

Cited by 1 publication

References 23 publications

Superiority of Spaced Seeds for Homology Search

Superiority of Spaced Seeds for Homology Search

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