Dekel Tsur

Sequencing by Hybridization (SBH) is a method for reconstructing a DNA sequence based on its k-mer content. This content, called the spectrum of the sequence, can be obtained from hybridization with a universal DNA chip. The main shortcoming of SBH is that it reliably reconstructs only sequences of length at most square root of the size of the chip. Frieze et al. [9] showed that by using gapped probes, SBH can reconstruct sequences with length that is linear in the size of the chip. In this work we investigate the optimal placement of the gaps in the probes, and give an algorithm for finding nearly optimal gap placement. Using our algorithm, we obtain a chip design which is more efficient than the chip of Frieze et al.