Research Article
Efficient Serial and Parallel Algorithms for Selection of Unique Oligos in EST Databases
Algorithm 1
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 1 digit | | (6) the numbers in in base 10 | | (7) list of each for all | | (8) goo2() | | (9) end for |
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