Compare nucleotides across aligned sequences

Question

[brimaloney]

I have sequences for a gene of interest across multiple species that I hope to run a comparison for of each nucleotide in a sequence across every other, comparing base pairs of 1-2, 2-3, 1-3, ect.

I would also like to exclude any regions where the sequence had to fill in gaps or where there is poor alignment, noted by "-". Is there any command in biopython I could use as a starting point for this?

[finswimmer]

Hello,

can you please give an example how your input looks like and how your output should look like?

fin swimmer

[brimaloney]

seq1: aactgta--tc seq2: aaatgtat-cc output: aaxtgta--xc x marking where there is a difference between the sequences, - marking where at least 1 of the pairs does not have information at that position

[finswimmer]

Hello,

you can just iterate over each position in both sequences and compare the character:

seq1 = "aactgta--tc"
seq2 = "aaatgtat-cc"

output = ''

for a, b in zip(seq1, seq2):
    if (a == b) and '-' not in (a, b):
        output += a
    elif '-' in (a, b):
        output += '-'
    else:
        output += 'x'

print(output)

fin swimmer

[cpad0112]

multiple pairwise sequence alignment?

pairwise alignment for multiple sequences in a file

[brimaloney]

the sequences are already aligned i would like to just pull out the positions where there is a mismatch in the basepairs at a given position between each pair of sequences