Check Oligonucleotides Against Database: how it works

By now you should have a set of potentially useful oligonucleotides to screen against the database constructed earlier.  The screening step works as follows:

A sequence is extracted from the database. Each oligonucleotide is checked for a direct match with this sequence.  If a match is successful, the oligonucleotide is retained and the successful match recorded.  If unsuccessful, the oligonucleotide is discarded.  The same process is then repeated with the next sequence, and so on, until no sequences remain.  For an oligonucleotide to match successfully, canonical bases (A, C, G, U, T) must match with themselves, whilst degenerate bases (B, D, H, K, M, N, R, S, V, W and Y) match with themselves or with the canonical bases they represent.