Research Article

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

Algorithm 3

Algorithm for the unique oligos problem.
Require: EST database , integer (length of unique oligos) and integer
     (maximum number of mismatches between non-unique oligos)
Ensure: All unique -mers in
(1)
(2) findqmers( ) (hashtable of positions of all qmers in )
(3) for   to split loop iterations among processors}  do
(4) as a base 4 integer of length
(5) list of base 4 integers of length mismatching by at most 2 digits
(6) the numbers in in base 10
(7) list of each for all
(8) goo2( )
(9) end for