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Week1-ProtienSequence-GlobalAlignment.py
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Week1-ProtienSequence-GlobalAlignment.py
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# -*- coding: utf-8 -*-
"""
Created on Fri Jun 29 14:38:00 2018
@author: KanzaBatool
"""
from Bio import pairwise2
from Bio.pairwise2 import format_alignment
from Bio.Seq import Seq
#bring dna sequence into our main code to keep things clean
dna = "GGTTCCGTGATGCACAGCTCCTTGGTTTTAATGAGTGTTTGTGAATGCAGTTGGTGAAGAACTCAGGCGAGCAGAGGCAATTGTGGACACCCCTACAGAAACGTCCTATACCCATGTGGCAATGCTCTGAAGAATAGCAGGGACCTCAGGAATGTCTATGGCCATACAATGACTAAACCAAATTCCCTCATCTTCTACTGTATCATTGTTTTAGGACTGACACTTATGAAAATCCAATTATCTGAGGAATGTGAGCTTATCATAAAGAGGCCAAACGCAAACCTTACCAGAGTGCCCAAGGACCTACCCTTGCAAACAACTACTTTAGATCTATCACAAAACAATATATCTGAGCTTCAGACTTCTGACATCCTCTCATTGTCCAAGCTGAGGGTCCTGATAATGTCCTACAACAGACTCCAGTATCTTAATATCAGTGTTTTCAAATTCAACACAGAGCTGGAATATTTGGATTTGTCCCACAATGAGCTAAAGGTGATCTTGTGCCACCCAACAGTCAGCCTCAAGCATTTGGACCTCTCCTTTAATGCCTTTGATGCCCTGCCTATATGCAAAGAATTTGGCAACATGTCCCAACTACAGTTCCTGGGGTTGAGCGGTTCTCGGGTACAAAGTTCAAGTGTGCAGCTGATTGCTCATTTGAACATCAGTAAGGTTTTGCTGGTGTTAGGAGATGCTTATGGGGAAAAAGAAGACCCCGAATCTCTTCGGCACGTTAGCACTGAGACTCTGCATATTGTTTTCCCGTCGAAAAGAGAATTCCGTTTTCTTCTGGATGTGTCCGTCAGCACTACGATCGGTTTGGAACTGTCTAACATCAAGTGTGTGCTTGAAGACCAGGGCTGCTCTTATTTCTTACGTGCTTTGTCAAAGCTTGGAAAGAATCTGAAGCTCTCAAATCTTACCCTGAACAATGTGGAAACAACGTGGAATTCCTTCATTAATATCCTCCAGATAGTTTGGCATACGCCAGTCAAATATTTCTCAATTTCAAATGTGAAGCTACAAGGTCAACTTGCCTTCAGGATGTTCAATTATTCTGACACTTCTCTGAAGGCTTTGTCGATACATCAAGTTGTCACTGATGTCTTCAGCTTCCCCCAAAGTTACATATACAGTATCTTTGCCAATATGAACATCCAAAACTTTACAATGTCTGGAACACACATGGTCCACATGCTGTGCCCGTCCCAAGTTAGCCCATTTCTGCATGTGGACTTTACAGATAACCTTTTAACAGACATGGTTTTTAAAGACTGTAGAAACTTAGTTAGATTGAAAACACTTAGTTTACAAAAGAATCAGTTAAAAAACCTTGAGAATATAATCCTCACATCTGCAAAGATGACATCCCTACAAAAACTAGACATTAGCCAGAATTCTCTAAGGTACAGCGATGGGGGAATCCCATGCGCCTGGACCCAGAGTTTGTTAGTTTTAAATTTGTCTTCGAATATGCTTACAGGCTCTGTCTTCAGATGCTTACCTCCCAAAGTCAAGGTCCTTGACCTTCACAACAACAGGATAATGAGCATCCCTAAAGATGTCACCCACCTGCAGGCTTTGCAGGAACTCAATGTAGCATCCAACTCCTTAACTGACCTTCCTGGGTGCGGGGCCTTCAGCAGCCTTTCTGTGCTGGTCATCGACCATAACTCAGTTTCCCATCCCTCTGAGGATTTCTTCCAGAGCTGTCAGAATATTAGATCCCTAACAGCGGGAAACAACCCATTCCAATGCACATGTGAGCTGAGGGACTTTGTCAAGAACATAGGCTGGGTAGCAAGAGAAGTGGTGGAGGGCTGGCCTGACTCTTACAGGTGTGACTACCCAGAAAGCTCTAGGGGAACTGCACTGAGGGACTTCCACATGTCTCCACTATCCTGTGATACTGTTCTGCTGACTGTCACCATCGGGGCCACTATGCTGGTGCTGGCTGTCACTGGGGCTTTCCTCTGTCTCTACTTTGACCTGCCCTGGTATGTGAGGATGCTGTGTCAGTGGACACAGACCAGGCACAGGGCCAGGCACATCCCCTTAGAGGAACTCCAGAGAAACCTCCAGTTCCATGCTTTTGTCTCATACAGTGGGCATGATTCTGCCTGGGTGAAGAACGAATTACTACCCAACCTAGAGAAAGATGACATCCAGATTTGCCTCCATGAGAGGAACTTTGTCCCTGGCAAGAGCATTGTGGAGAACATCATCAATTTCATTGAGAAGAGTTACAAGTCCATCTTTGTGCTGTCTCCCCACTTCATCCAGAGTGAGTGGTGTCATTATGAACTCTATTTTGCCCATCACAATCTCTTCCATGAAGGCTCTGATAACTTAATCCTCATCTTGCTGGCACCCATTCCCCAGTACTCCATCCCTACCAATTACCACAAGCTCAAAACTCTCATGTCACGAAGGACCTATCTGGAATGGCCCACAGAGAAGAACAAGCATGGACTTTTTTGGGCAAACCTAAGAGCATCCATTAATGTTAAGCTGGTTAACCAGGCAGAAGGAACGTGTTACACACAGCAATAAGAATATCCACC"
def loop():
coding_dna = Seq(dna)
orf1 = coding_dna.translate()
print ("**********************ORF1***********************")
print (orf1)
print ("\n\n")
coding_dna = Seq(dna[1:])
orf2 = coding_dna.translate()
print ("**********************ORF2***********************")
print (orf2)
print ("\n\n")
coding_dna = Seq(dna[2:])
orf3 = coding_dna.translate()
print ("**********************ORF3***********************")
print (orf3)
print ("\n\n")
coding_dna = Seq(dna)
coding_dna_reverse_comp = coding_dna.reverse_complement()
orf4 = coding_dna_reverse_comp.translate()
print ("**********************ORF4***********************")
print (orf4)
print ("\n\n")
coding_dna = Seq(dna[:-1])
coding_dna_reverse_comp = coding_dna.reverse_complement()
orf5 = coding_dna_reverse_comp.translate()
print ("**********************ORF5***********************")
print (orf5)
print ("\n\n")
coding_dna = Seq(dna[:-2])
coding_dna_reverse_comp = coding_dna.reverse_complement()
orf6 = coding_dna_reverse_comp.translate()
print ("**********************ORF6***********************")
print (orf6)
print ("\n\n")
def match():
String1 = 'ACCGTTTTTTACACAC'
String2 = 'ACGACACGTAC'
alignments = pairwise2.align.globalxx(String1, String2)
print(format_alignment(*alignments[0]))
def main():
loop()
match()
main()