The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
Application of a superword array in genome assembly
Open accessAbstract
We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array. We describe simple algorithms for constructing and using a superword array to find pairs of sequences that share a unique superword. The algorithms are implemented in a genome assembly program called PCAP.REP for computation of overlaps between reads. Experimental results produced by PCAP.REP and PCAP on a whole-genome dataset show that PCAP.REP produced a more accurate and contiguous assembly than PCAP.
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A total of approximately 1.2 million single nucleotide polymorphisms (SNPs) were identified within the 1.84-Gb sequenced female platypus genome using two independent analyses, SSAHA2 and PCAP output.
“We identified a total of , 1.2 million single nucleotide polymorphisms (SNPs) within the 1.84-Gb sequenced female platypus genomeusing two independent analyses, SSAHA2 (SSAHA: a fast search method for large DNA databases 72 ) and PCAP output 20 (Supplementary Notes 11).”
From Genome analysis of the platypus reveals unique signatures of evolution (2008) · cites this paper as [20]
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Research works printed but not linked: 1
- [4]Batzoglou S. Jaffe D. Stanley K. Butler J. Gnerre S. Mauceli E. Berger B. Mesirov J.P. Lander E.S. ARACHNE: a whole-genome shotgun assembler Genome Res. 2002 12 177 189 11779843 PMC155255
Cited by
Sorted by citations
Genome analysis of the platypus reveals unique signatures of evolution
paper, A. L. O. A. A. T. A. A. A. T. E. O. T. (2008) · Nature · doi:10.1038/nature06936 · Cited by 719
Metadata
- Authors
- Huang, X.
- Affiliations
- Iowa State University (US)
- Corresponding author
- Huang, X.
- ORCID
- Huang, X.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-01-08
- Volume
- 34
- Issue
- 1
- Pages
- 201-205
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1325203
- OpenAlex
- W2103052607
- Cited by
- 30
- References
- 30
- Citations by year
- 2019: 1 · 2017: 1 · 2016: 1 · 2015: 2 · 2014: 5 · 2012: 1
- FWCI
- 4.56
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- other-oa
- Locations
- Nucleic Acids Research (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Digital Commons@Becker (Washington University School of Medicine) (submittedVersion, other-oa)
- Iowa State University Digital Repository (Iowa State University) (submittedVersion, other-oa)
- Funders
- Iowa State University
- National Institutes of Health
- National Human Genome Research Institute (U54HG003079)
- Topics
- Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- genome assembly, sequence matching, suffix arrays, look-up table, PCAP, whole genome sequencing
- MeSH terms
- Algorithms, Histoplasma, Genome, Fungal, Computational Biology, Genomics
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