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.