Journal
NUCLEIC ACIDS RESEARCH
Volume 34, Issue 1, Pages 201-205Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkj419
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Funding
- NHGRI NIH HHS [U54 HG003079] Funding Source: Medline
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [U54HG003079] Funding Source: NIH RePORTER
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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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