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Published online 18 February 2004

Nucleic Acids Research, 2004, Vol. 32, No. 3 1208-1213
© 2004 Oxford University Press

A gene-specific DNA sequencing chip for exploring molecular evolutionary change

Olivier Fedrigo and Gavin Naylor*,1

Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA and 1 School of Computational Science and Information Technology (CSIT), Florida State University, Tallahassee, FL 32306-4120, USA

*To whom correspondence should be addressed. Tel: +1 850 645 0314; Fax: +1 850 644 0098; Email: naylor{at}csit.fsu.edu

Sequencing by hybridization (SBH) approaches to DNA sequencing face two conflicting constraints. First, in order to ensure that the target DNA binds reliably, the oligonucleotide probes that are attached to the chip array must be >15 bp in length. Secondly, the total number of possible 15 bp oligonucleotides is too large (>415) to fit on a chip with current technology. To circumvent the conflict between these two opposing constraints, we present a novel gene-specific DNA chip design. Our design is based on the idea that not all conceivable oligonucleotides need to be placed on a chip— only those that capture sequence combinations occurring in nature. Our approach uses a training set of aligned sequences that code for the gene in question. We compute the minimum number of oligonucleotides (generally 15–30 bp in length) that need to be placed on a DNA chip to capture the variation implied by the training set using a graph search algorithm. We tested the approach in silico using cytochrome-b sequences. Results indicate that on average, 98% of the sequence of an unknown target can be determined using the approach.


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