Abstract

Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a ‘ well-established biological and computational method used in practice. Many conventional algorithms for shotgun sequencing are based on the notion.of pairwisk fragment overlap. * While shotgun sequencing infers a DNA sequence given the sequences of overlapping frag-ments, a recent and complementary method, called sequencing by hybridization (SBH), in-fers a DNA sequence given the set of oligomers that represents all subwords of some fixed length, k. In this paper,. we propose a new computer algorithm for DNA sequence assembly that combines in a novel way the techniques of both shotgun and SBH methods. Based on our preliminary investigations, the algorithm promises- to be very fast and practical for DNA sequence assembly.

Citations