Question

Complete a) flowchart solution and b) working Python solution. It will need to compare gene sequences, looking for differences (mutations), keeping track of how many are different and will include clear two-part output: indicating if the ‘baby’ has the mutation for diabetes or not, and the identity between the siblings’ sequences.

BABY:

ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCTGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAG

BROTHER:

ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAG

Does the ‘baby’ carry the mutation associated with diabetes?
Which (what number) nucleotide has mutated?
What is the ‘identity” of the siblings’ sequences? In other words, find the percentage, to one decimal place, describing how similar those two are.

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So far I have this:

def find_mutation_location(nuc1, nuc2):
n = len(nuc1)
for i in range(0,n,3):
if nuc1[i:i+3] != nuc2[i:i+3]:
return (i+1)//3
  
n1 = "ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCTGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAG"
n2 = "ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAG"
print(find_mutation_location(n1,n2))

def calculate_similarity(nuc1, nuc2):
n = len(nuc1) // 3
different = 0
for i in range(0,n,3):
if nuc1[i:i+3] != nuc2[i:i+3]:
different += 1
print(calculate_similarity(n1,n2))

I seem to have been able to locate the mutation at nucleotide number 54, but am having issues with calculating the similarity to a percentage/1 decimal point. Please advise, and also provide working flow-chart solution if possible. Thanks!

Answer 1

Many changes are done in code.

CODE:

def find_mutation_location(nuc1, nuc2):

n = len(nuc1)

pos=[] # position list to store all mutation

for i in range(0,n,3):

if nuc1[i:i+3] != nuc2[i:i+3]:

pos.append((i+1)//3) # adding the position in the list

return pos # returning list

n1 = "ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCTGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAG"

n2 = "ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAG"

print(*(find_mutation_location(n1,n2))) # * is use to print items in list in a string

def calculate_similarity(nuc1, nuc2):

n = len(nuc1) # calculating DNA length

total =0 # total gene set

similar =0 # similar gene set

for i in range(0,n,3):

total = total +1 # adding 1 in total every time loop is executed

if nuc1[i:i+3] == nuc2[i:i+3]: # if similar gene set

similar = similar +1 # add 1 to number of similar gene set

return similar/total*100 # returning percentage

print("{:.1f}%".format(calculate_similarity(n1,n2))) # .format is use to print percentage upto 1 decimal place

Go through screentshot for indentation.

OUTPUT:

FLOWCHART: