An Almost Quadratic Time Algorithm for Sparse Spliced Alignment

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7 Citations (Scopus)


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(n2.25) time, or very recently, in O(n2log 2n) time, by proposing an O(n2log n)-time algorithm.

Original languageEnglish
Pages (from-to)189-210
Number of pages22
JournalTheory of Computing Systems
Issue number1
Publication statusPublished - 2011 Jan


  • Common substring alignment
  • Semi-local string comparison
  • String algorithm

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computational Theory and Mathematics


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