An Almost Quadratic Time Algorithm for Sparse Spliced Alignment

Authors:
Yoshifumi Sakai
Affiliations:
Tohoku University, Graduate School of Agricultural Science, 1-1 Amamiya-machi, 981-8555, Tsutsumidori, Aoba-ku, Sendai, Japan
Venue:
Theory of Computing Systems
Year:
2011

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Abstract

The sparse spliced alignment problem consists of finding a chain of zero or more exons from O(n) prescribed candidate exons of a DNA sequence of length O(n) that is most similar to a known related gene sequence of length n. This study improves the running time of the fastest known algorithm for this problem to date, which executes in O(n 2.25) time, or very recently, in O(n 2log 2 n) time, by proposing an O(n 2log n)-time algorithm.