CODEHOP:
COnsensus-DEgenerate Hybrid Oligonucleotide Primers

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Degeneracy strictness

Degeneracy strictness specifies how to count nucleotide(s) with low occurrences. A nucleotide will be counted if the ratio of its frequency value over the highest (maximal) value in that position is more or equal to the strictness. Strictness can have values between 0 and 1. Strictness of 0 will cause all the nucleotides that actually appear in the position to be counted. Strictness of 1 means that only the nucleotides with the highest value in a position will be counted. Intermediate strictness values give behavior in between.

examples:
1 2 3 4 5
base value ratio value ratio value ratio value ratio value ratio
A 0 0 25 1 40 0.67 30 0.67 45 1
C 0 0 25 1 0 0 5 0.11 11 0.24
G 100 1 25 1 60 1 45 1 17 0.38
T 0 0 25 1 0 0 20 0.44 27 0.6
Strictness degeneracy
0 1 4 2 4 4
0.33 1 4 2 3 3
0.5 1 4 2 2 2
0.67 1 4 2 2 1
1 1 4 1 1 1
The highest base frequency value(s) in each of the 5 examples is underlined.

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Page last modified Jan 1998