Question

Write Matlab or Python scripts to solve. Output the aligned sequences with the maximum alignment score.

We would like to align two DNA sequences: (v) C G A T A C T, and (w) G A T T C G T based on the following scoring scheme as discussed in class:

i) s(i, j) = 1 if vi = wj (matches);

ii) s(i, j) = 0 if vi != wj (mismatches);

iii) d = 0 (indels: insertions or deletions).

What would be the maximum alignment score? Explain how you get the result.

Answer 1

The maximum Alignment Score is 5.

There are 2 ways of alignment:

Global Alignment: Where you take both entire sequences into account and find the alignment

Local Alignment: Where u take a small segment into consideration

# is used for comments. This is not a part of the code. The comment is used to give a clear understanding of the code.

The code is as:

pip3 install biopython #For installing the library named 'Biopython'

from Bio import pairwise2 #for Importing pairwise Module.
from Bio.pairwise2 import format_alignment
X= 'CGATACT' #your DNA sequence 1
Y = 'GATTCGT' #your DNA sequence 2

#Local alignment
alignments = pairwise2.align.localxx(X, Y)  

for a in alignments:
print(format_alignment(*a))

#Global Alignment

align = pairwise2.align.globalxx(X,Y)
for a in align:
print(format_alignment(*a))