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What is 'k' in sequencing?

Bioinformatics Asked on December 11, 2020

When a DNA sequence is sequenced, I’ve only ever dealt with A,T,C,G and N which indicates un-identifiable bases. However, I came across a ‘k’ recently and I had asked another researcher who gave me an answer for what ‘k’ represents but I don’t quite recall. It can’t just be an anomaly in that one sequence file. Any ideas?

2 Answers

See IUPAC codes:

IUPAC codes

So, as you can see above, K means "Either G or T".

Correct answer by user6690 on December 11, 2020

It is recommended you learn the degenerate nucleotide code. In sequencing it can signify poor quality sequence data, but in primer design it is useful. R (mutation within purines) and Y (mutation within pyrimidines) are common. K, a purine to pyrimadine or pyrimadine to purine mutation is, in my opinion, rare. I would treat a K mutation with caution and consider the triplet codon around it, i.e. if it is part of a protein gene.

Most phylogeneitcs programs will work with the degenerate nucleotide code, so in theory you can still obtain useful information with it.

Answered by Michael on December 11, 2020

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