What do GGN, AAP, TCN, CAP, CCN, TGQ, etc. mean in DNA analysis?

Question

What do the letters Y, Q, P and N mean in three-letter combinations involving DNA and/or RNA? I know, of course, about the bases A, C, G, T and U but especially in articles (and forensic tv shows) I see, they are connected to three-letter amino acid codes, letter combos like GTN, GGN, etc. What do they mean?

Answer 1

It is not always possible to obtain an absolutely precise result from automated DNA sequencers, mostly due to too much background noise or two very close peaks which the computer has difficulty reading.

An example of a very noisy four-color chromatogram from a sequencer (sanger):

As you would notice, there are several ambiguous spots and the computer algorithm can be confused or mis-call the wrong nucleotide. Often humans are called in to resolve such ambiguities. It's a fairly common practice.

Sometimes the ambiguity goes beyond a solid conclusion, like when two or more peaks have almost the same intensity.

In that case it is better to explicity label those ambiguous nucleotides as either, say A or B, rather than report a possibly incorrect sequence. Thus was born the incompletely specified nucleic acids.

Here's where IUPAC comes in: the single letter code recommendations.

The "N" in GGN, TCN and CCN would mean the third codon was completely ambiguous and could be any one of tbe four bases. Y would mean pyrimidine (C, U or T).

This would satisfy your query with the exception of the letters P and Q, which I assume were wrongly picked up, or the code was for proteins (amino acid) sequence single letter code.