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I'm currently looking protocol for PAT-seq, and when it talks about the barcoding that's utilized, the documentation mentions there being an "N" and "NN" in the sequence, as well as a "V". For example:

...CCGATCTNNxxxTTT...TTTVN

where the "..." is an abbreviation of the the sequence and the "xxx" is the location of the barcode sequence.

As you can see, there's an "NN" just before the barcode sequence, and then, at the end of the T sequence there's a "VN". It says that the "NN" serves to affirm that the reads obtained are derived from different RT reactions and not all from a single RT product that's been excessively amplified.

So, I'm guessing that the "N" just stands for an undetermined nucleotide. Is that right? But then, what about the "V"?

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It is standard IUPAC nomenclature to write bases that are not uniquely defined.

For example, "N" means "any base", but "V" means "A, C or G, but not T".

See the full list here

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