Question

Can I get help in making a small program in python implementing the Brute force motif search algorithm?

Answer 1

Brute_Force_Motif_Search(Dna,k)-Every possibility of  k-mers Motifs from Dna.

Code-

def BruteForce(Dna, k): # function definition with parameter Dna and k-mers Motifs
occurrences = []
for i in range(len(Dna)-len(k)+1): # loop over alignment
match = True
for j in range(len(k)): # loop over characters
if Dna[i+j] != k[j]: # compare characters
match = False # mismatch
break
if match: # allchars matched
occurrences.append(i)

print(occurrences)
k = input("Enter k-mers Motifs: ")
Dna = input("Enter Dna sequence: ")
BruteForce(Dna, k)

Output-

Enter k-mers Motifs: AGAGA

Enter Dna sequence: AGATAGAGAGATAGAGAGATAGAGAGATAGAGAGATAGAG
[4, 6, 12, 14, 20, 22, 28, 30]

Output-