Figure 1. Sequencing failure due to degenerate solutions.

Classical sequencing by hybridization of three representative 509-mer target sequences taken from a benchmark library [15] using 10-mer probes. For each target sequence, 10 independent reconstruction attempts using a state-of-the-art heuristic algorithm (ACO [12]) are simulated and the results are visualized with grey (pink) color representing bases that are correctly (incorrectly) matched by the reconstruction. Reconstruction failures are correlated with the locations of 9-mer but not with 10-mer repeats within the target sequence, shown in the upper two rows of each figure. For two interlaced 9-mer repeats (C), two different solutions with Needleman-Wunsch similarity score [17] between the target and the reconstruction of 509 and 128 are found. Both sequences have the same 10-mer probe spectrum and can thus not be distinguished using classical SBH. For reconstruction attempts of other target sequences see the online applet [16] and instructions in the information S1.