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Nucleic Acids Research 2006 34(1):201-205; doi:10.1093/nar/gkj419
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Published online 5 January 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

Application of a superword array in genome assembly

Xiaoqiu Huang*, Shiaw-Pyng Yang1, Asif T. Chinwalla1, LaDeana W. Hillier1, Patrick Minx1, Elaine R. Mardis1 and Richard K. Wilson1

Department of Computer Science, Iowa State University Ames, IA 50011, USA 1Genome Sequencing Center, Washington University School of Medicine St Louis, MO 63108, USA

*To whom correspondence should be addressed at Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011-1040, USA. Tel: +1 515 294 2432; Fax: +1 515 294 0258; Email: xqhuang{at}cs.iastate.edu

Received October 3, 2005. Revised November 9, 2005. Accepted December 13, 2005.

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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