Faster exon assembly by sparse spliced alignment

Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is spliced alignment, proposed by Gelfand et al., which scores different candidate exon chains within a DNA sequence of length m by comparing them to a known related gene sequence of length n, m = Θ(n). Gelfand et al. gave an algorithm for spliced alignment running in time O(n). Kent et al. considered sparse spliced alignment, where the number of candidate exons is O(n), and proposed an algorithm for this problem running in time O(n). We improve on this result, by proposing an algorithm for sparse spliced alignment running in time O(n). Our approach is based on a new framework of quasi-local string comparison.