Designing Efficient Spaced Seeds for SOLiD Read Mapping

Algorithm 1

Lossless property verification algorithm.

Input

  𝑚 = read length

  𝒬 = the seed automaton

  𝑘 = the threshold for the number of mismatches

foreach iteration 𝑖∈[1⋯𝑚]  do

  foreach state 𝑞 of 𝒬  do

    Compute the minimal number of mismatches needed to reach 𝑞 at step 𝑖;

  end

end

The lossless condition holds iff at step 𝑚, all nonfinal states have a number of

mismatches greater than 𝑘.