Article
Application of a superword array in genome assembly
Nucleic Acids Research
Document Type
Article
Disciplines
Publication Version
Published Version
Publication Date
1-1-2006
DOI
10.1093/nar/gkj419
Abstract
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.
Rights
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Copyright Owner
The Authors
Copyright Date
2006
Language
en
File Format
application/pdf
Citation Information
Xiaoqiu Huang, Shiaw-Pyng Yang, Asif T. Chinwalla, LaDeana W. Hillier, et al.. "Application of a superword array in genome assembly" Nucleic Acids Research Vol. 34 Iss. 1 (2006) p. 201 - 205 Available at: http://works.bepress.com/xiaoqiu-huang/17/
This article is published as Huang, Xiaoqiu, Shiaw-Pyng Yang, Asif T. Chinwalla, LaDeana W. Hillier, Patrick Minx, Elaine R. Mardis, and Richard K. Wilson. "Application of a superword array in genome assembly." Nucleic acids research 34, no. 1 (2006): 201-205. doi: 10.1093/nar/gkj419.