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Rapid Homology Search with Two-Stage Extension and Daughter Seeds
[chapter]
2005
Lecture Notes in Computer Science
Using a seed to rapidly "hit" possible homologies for further examination is a common practice to speed up homology search in molecular sequences. It has been shown that a collection of higher weight seeds have better sensitivity than a single lower weight seed at the same speed. However, huge memory requirements diminish the advantages of high weight seeds. This paper describes a twostage extension method, which simulates high weight seeds with modest memory requirements. The paper also
doi:10.1007/11533719_13
fatcat:szlgvb5kpzgopktmxuw6qmk27e