Hi friends,

Is there a way to develop a PWM for dinucleotide sequence and trinucleotide sequence

I have coloumn of sequnces which has same string length that is approx 30 nt, I want to develop a method which would tell me the whether the di nucleotide is present in position 1 or not

as example

suppose

a = "(ATATAGCGCA","ATATATGGCC")

I need to know whether AT is present in position 1 or not ,like wise subsequent presence of dinucleotides and make a matrix out of them

it would be really great if you could help me