Application of a superword array in genome assembly.
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.
Huang
Xiaoqiu
X
Department of Computer Science, Iowa State University, Ames, IA 50011-1040, USA. xqhuang@cs.iastate.edu
Yang
Shiaw-Pyng
SP
Chinwalla
Asif T
AT
Hillier
LaDeana W
LW
Minx
Patrick
P
Mardis
Elaine R
ER
Wilson
Richard K
RK
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods*; D006658:Histoplasma / Q000235:genetics