To understand Punnett Squares

[ardmore]

Hello,

I have difficult to understand 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.

[HESmith]

You are correct that 'A' and 'a' do not refer to the actual nucleotide, but represent the dominant and recessive alleles, respectively. However, the different alleles are not limited to single nucleotide differences, and can include insertions, deletions, and more complex rearrangements. So, 'AA' represents two copies of the same (dominant) allele, 'aa' represents two copies of the recessive allele, and 'Aa' represents one copy of each.

[ardmore]

Can you please look at http://pngu.mgh.harvard.edu/~purcell...data.shtml#ped
It says

Genotypes (column 7 onwards) should also be white-space delimited; 
they can be any character (e.g. 1,2,3,4 or A,C,G,T or anything else) except 0 
which is, by default, the missing genotype character. All markers should be 
biallelic. All SNPs (whether haploid or not) must have two alleles specified. 
Either Both alleles should be missing (i.e. 0) or neither. No header row should 
be given. For example, here are two individuals typed for 3 SNPs (one row = 
one person): 
     FAM001  1  0 0  1  2  A A  G G  A C 
     FAM001  2  0 0  1  2  A A  A G  0 0

So in this situation, can we say an allele is jsut a nucleotide coincidently?