Snp Ambiguous Alleles

Question

[win]

Hi there, Hoping someone can help. I have sequences from -ve strand and i also have the reference and variant alleles at certain location on the strand.

For e.g. the strand could be AGGTAATATATC and the SNP alleles are A and T.

I want to convert this strand into forward strand, which is simple, convert to reverse complimentary. When doing this do the two alleles A and T also follow suite i.e. A becomes T and T becomes A, i am asking because A and T are ambiguous.

Just wanting to make sure this is the case, help will be greatly appreciated.

Thanks, A

Answer 1

[pagel]

Yes, but in your case where there's a single nucleotide difference, it doesn't matter one way or the other (assuming equal penetrance of A and T). If unequal amounts of the two, if you have GaA at 75% and GtA at 25%, the rev-comp is TtC 75%, TaC 25%.

The rev-comp of W (A/T) is W (T/A). Similarly the rev-comp of S (G/C) is S (C/G).

rev-comp of Y (C/T) is R (G/A).