Efficient Serial and Parallel Algorithms for Selection of Unique Oligos in EST Databases

Algorithm 2

Algorithm for the unique oligos problem.

Require: EST database 𝐷={𝑥₁,𝑥₂,…,𝑥_𝑘}, integer 𝑙 (length of unique oligos) and integer 𝑑

     (maximum number of mismatches between non-unique oligos)

Ensure: All unique 𝑙-mers in 𝐷

(1) 𝑞←𝑙/(𝑑+1)

(2) 𝑝𝑜𝑠𝑖← findqmers(𝑞) (hashtable of positions of all qmers in 𝐷)

(3) for  𝑖←1 to 4^𝑞{split loop iterations among processors}  do

(4) goo(𝑞,𝑙,𝑑,𝑝𝑜𝑠𝑖[𝑖])

(5) end for