Work

Application of a superword array in genome assembly

Year: 2006

Type: article

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.

Source: Nucleic Acids Research

DOI: 10.1093/nar/gkj419

Author: X. Huang

Institution: Iowa State University

Language: English

Topic: Algorithms and Data Compression

Subfield: Theoretical Computer Science

Field: Mathematics

Domain: Physical Sciences

Open Access status: gold

Estimated APC paid: $3,992

Funders: Iowa State University, National Institutes of Health, National Human Genome Research Institute