comparison of two dna sequences

[Palermo79]

Hi,
I would ike to compare two dna sequences. let's say
seq_a= TGGAGGCAATGGCGGCCAGCACTTCCCTGCCTGACCCTGGAGACTTTGAC CGGAACGTG
CCCCGGATCTGTGGGGTGTGTGGAGACCGAGCCACTGGCTTTCACTTCAA TGCTATGACC
TGTGAAGGCTGCAAAGGCTTCTTCAGGCGAAGCATGAAGCGGAAGGCACT ATTCACCTGC
CCCTTCAACGGGGACTGCCGCATCACCAAGGACAACCGACGCCACTGCCA GGCCTGCCGG

and

seq_b=GACTCCTCCTCCTCCTGCTCAGATCACTGTATCACCTCTTCAGA CATGATGGAC---TCGTCCTTCTCCCTGCTGAATGAAAAATCAGATGACTCT---------------GTGCTAGAG
CTGTCCCAA-------------------------------------------------------------------------------------GACCTCACCTCTGAGGACCAGATCGTACTGCTGAAGTCAAGTGCCATTGA GGTCATCATGTTGCGCTCCAATGAGTCCTTCACC

how can I find differences in term of codons and position?

[Mariostg]

How does your program look so far?
What output do you expect based on your two sequences.
There are different ways to present a solution. So more details are required.

[Palermo79]

Hi, right now I done the script to find mismatches between those sequences as follow:
def sequence_compare(seq_a, seq_b):
len1= len(seq_a)
len2= len(seq_b)
mismatches = []
for pos in range (0,min(len1,len2)) :
if seq_a[pos] != seq_b[pos]:
mismatches.append(pos)
return mismatches
sequence_compare(seq_a,seq_b)

Thus eventually this gives me the right position of the mismatches between those two sequence. But at this point I get lost, because I want to know which codons are involved in comparison.
i.e I know that there is a mismatch at the position 19 but which codons is involved so far?, and what the related amino acid?
thanks

[Mariostg]

Maybe something like this would help:

def sequence_compare(seq_a, seq_b):
        len1= len(seq_a)
        len2= len(seq_b)
        mismatches = []
        for pos in range (0,min(len1,len2)) :
              if seq_a[pos] != seq_b[pos]:
                  mismatches.append('|')
              else:
                  mismatches.append(' ')
        print (seq_a)
        print (mismatches)
        print (seg_b)
sequence_compare(seq_a,seq_b)
 
Would print and show the differences.
 
ACTGGCT
 |  | |
ATTGACA
 

[Palermo79]

ok cool I am gona try immediately...

thanks!

[Palermo79]

ok it works quite nicely but what about if I want in addition to this I want to know the amino acid related to that specific codons change?

thanks

[Mariostg]

I guess it all depends on how you want to visualize the output. Maybe add something similar to what I proposed earlier but instead of appending pipe and space characters, add a new list with the related amino acid.