A new algorithm for DNA sequence assembly - PubMed (original) (raw)
Comparative Study
. 1995 Summer;2(2):291-306.
doi: 10.1089/cmb.1995.2.291.
Affiliations
- PMID: 7497130
- DOI: 10.1089/cmb.1995.2.291
Comparative Study
A new algorithm for DNA sequence assembly
R M Idury et al. J Comput Biol. 1995 Summer.
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.
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