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.
Keywords
Shotgun sequencingSequencing by hybridizationShotgunDNA sequencingSequence (biology)Sequence assemblyk-merHybrid genome assemblyAlgorithmComputational biologyDNAComputer scienceAlignment-free sequence analysisDNA nanoball sequencingBiologyGeneticsSequence alignmentBase sequenceDNA sequencerGeneGenomic libraryPeptide sequence
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Publication Info
- Year
- 1995
- Type
- article
- Volume
- 2
- Issue
- 2
- Pages
- 291-306
- Citations
- 344
- Access
- Closed
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Cite This
Ramana M. Idury,
Michael S. Waterman
(1995).
A New Algorithm for DNA Sequence Assembly.
Journal of Computational Biology
, 2
(2)
, 291-306.
https://doi.org/10.1089/cmb.1995.2.291
Identifiers
- DOI
- 10.1089/cmb.1995.2.291