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© Oxford University Press

Software for DNA sequencing by hybridization

Igor Belyi 1 and Pavel A. Pevzner 2,3

1Transarc Corporation Pittsburgh, PA 15219
2Department of Mathematics and Computer Science, University of Southern California Los Angeles, CA 90089, USA

3To whom correspondence should be addressed. E-mail: ppevzner{at}hto.usc.edu

Sequencing by hybridization (SBH) is a promising alternative approach to DNA sequencing and mutation detection. Analysis of the resolving power of SBH involves rather difficult combinatorial and probabilistic problems, and sometimes computer simulation is the only way to estimate the parameters and limitations of SBH experiments.

This paper describes a software package, DNA-SPECTRUM, which allows one to analyze the resolving power and parameters of SBH. We also introduce the technique for visualizing multiple SBH reconstructions and describe applications of DNA-SPECTRUM to estimate various SBH parameters. DNA-SPECTRUM is available at http://www.hto.usc.edu/software/sbh/index.html.

Received on September 17, 1996; accepted on November 7, 1996

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