About Punnett Squares

Question

[Zhshqzyc]

Hello,

I have a stupid question for Punnett Squares. For example, let us define "A" as being the dominant normal allele and "a" as the recessive abnormal one. As carriers, you and your mate are both heterozygous (Aa). This disease only afflicts those who are homozygous recessive (aa).

My question: Is "A" or "a" just pronoun? "A" may come from one of "A", "G", "C", "T"? "a" also may come from one of "A", "G", "C", "T"?

So "Aa" is just a combination of two letters of "A","G","C" and "T"? "AA" or "aa" is just one of "AA","GG","CC" and "TT"?

Thanks.

[Ying W]

This is a bioinformatics forum so this question is a bit off topic. I don't think you understand the difference between alleles (Aa) and nucleotides (ACGT)

Answer 1

[Charles E. Grant]

The alleles in Punnett Squares represent a higher level of abstraction then a simple base change. They can represent just about any variation in a genome that is linked to a clear phenotype. They might represent a single base change, or they might represent insertions, deletions, inversions or copy numbers variations. A and a are just labels for two different versions of some portion of the genome.

[Charles E. Grant]

I've no idea, since I don't know anything about plink. If your question is really about the specific use of Punnett Squares in plink then you should edit your question to reflect that.

[Zhshqzyc]

Thank you very much. For the plink analysis http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped Can we say an allele is jsut a nucleotide coincidently?