Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers

@inproceedings{Orenstein2013DesignOS,
  title={Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers},
  author={Yaron Orenstein and Ron Shamir},
  booktitle={Bioinformatics},
  year={2013}
}
MOTIVATION Novel technologies can generate large sets of short double-stranded DNA sequences that can be used to measure their regulatory effects. Microarrays can measure in vitro the binding intensity of a protein to thousands of probes. Synthetic enhancer sequences inserted into an organism's genome allow us to measure in vivo the effect of such sequences on the phenotype. In both applications, by using sequence probes that cover all k-mers, a comprehensive picture of the effect of all… CONTINUE READING
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