Sequencing by Hybridization

Standard oligo chips can, at least theoretically, be used for sequencing. Let us prepare an oligo chip that contains all possible sequences of length k. These sequences are called k-mers. Practical values of k are 8-10. If we expose this chip to a solution containing some target DNA, the results will show which k-mers occur in the target sequence.

Note, that the k-spectrum is a multi-set. We assume that if a k-mer appears more than once, in the target DNA, the hybridization experiment will report the number of its occurrences. To date, this requirement is impractical.

For instance, for k=3:

  $$\begin{eqnarray*}{} \centering T & = & ATGCAGGTCCAG \\ S & = & \{ATG, AGG, CAG, GCA, GGT, GTC, TCC, TGC, CCA, CAG\} \end{eqnarray*}$$