The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
A New Algorithm for DNA Sequence Assembly
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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Cites
Rapid similarity searches of nucleic acid and protein data banks.
Wilbur, W. J., & Lipman, D. J. (1983) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.80.3.726 · Cited by 1,546
Cited by
An Eulerian path approach to DNA fragment assembly
Pevzner, P. A., Tang, H., & Waterman, M. S. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.171285098 · Cited by 1,352
Self-citationHow to apply de Bruijn graphs to genome assembly
Compeau, P. E. C., Pevzner, P. A., & Tesler, G. (2011) · Nature Biotechnology · doi:10.1038/nbt.2023 · Cited by 673
The fragment assembly string graph
Myers, E. W. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1114 · Cited by 424
De novo fragment assembly with short mate-paired reads: Does the read length matter?
Chaisson, M. J., Brinza, D., & Pevzner, P. A. (2009) · Genome Research · doi:10.1101/gr.079053.108 · Cited by 279
De novo assembly of short sequence reads
Paszkiewicz, K., & Studholme, D. J. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq020 · Cited by 204
Weather effects on human mobility: a study using multi-channel sequence analysis
Brum-Bastos, V. S., Long, J. A., & Demšar, U. (2018) · Computers, Environment and Urban Systems · doi:10.1016/j.compenvurbsys.2018.05.004 · Cited by 66
Metadata
- Authors
- IDURY, R. M., & WATERMAN, M. S.
- Venue
- Journal of Computational Biology
- Publisher
- SAGE Publications
- Published
- 1995-01
- Volume
- 2
- Issue
- 2
- Pages
- 291-306
- ISSN
- 1066-5277 (ISSN-L)
- 1557-8666
- OpenAlex
- W2022910024
- Cited by
- 342
- References
- 1
- FWCI
- 0.24
- Type
- journal article
- Language
- en
- Open access
- closed
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