A new algorithm for DNA sequence assembly

J Comput Biol. 1995 Summer;2(2):291-306. doi: 10.1089/cmb.1995.2.291.

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 pairwise fragment overlap. While shotgun sequencing infers a DNA sequence given the sequences of overlapping fragments, a recent and complementary method, called sequencing by hybridization (SBH), infers 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.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms*
  • Base Sequence*
  • DNA / chemistry*
  • Mathematics*
  • Models, Theoretical*
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Nucleic Acid Hybridization
  • Oligodeoxyribonucleotides*
  • Software

Substances

  • Oligodeoxyribonucleotides
  • DNA