Python bioinformations 101

dna.py

# Example of real-world use of Python string manipulation - DNA analysis
#
# DNA is made of ATGC
#
# A-T are always paired
# G-C are always paired
#
# So if you have a sequence of one side of a DNA molecule, can you use Python to generate the other side?
#


dna1 = 'ACCAGTACCAGTGT'
dna2 = 'GTACACCAGGTCTA'

# Remember
# A pairs with T   and     T pairs with A
# C pairs with G   and     G pairs with C

# so for dna1, it begins ACCA... so output string will start TGGT...

# In DNA, the A, T, C, G are codes for generating proteins
#   you are made of 100's of different kinds of proteins.
# Most of your DNA doesn't appear to make proteins - only about 1% of it encodes protein.
# A part of DNA that encodes a protein is called a gene So how do you find which parts do,
# or where are your genes in your DNA?
#
# So biologist are interested in where certain codes are. One code is ATG and this
# is called a 'start codon' and that means 'start making a protein here'
#
# Does string 1 have any genes in it?
# Does string 2 have any genes in it?
#
# If so, what's the index of where that gene is?

dna3 = 'ACGACGGATACGCGGGAGCTATTCATCTGTGTTGAGAAACACCGGAGAACTTATTGGTCTGTCAAGATTGCGACTGTGGTATAGCTCACCCGGTCGCGGCTTTCTAGT' \
       'TAGTGGCCAGCTCCCGTGTATTTGGAAGCTGAGAGAAGGACCCCTGTGGTTCGAATCAGCTCACGAGCGCTGGCACACCGCAATCAGCCGGCTAATAAAATTCGTACG' \
       'GACTGCCCCACACAAGAAGACGGTAAATTTATCAACACTATAGTTGCTATACACCAGGAGCGAGCGTAAATTTGTAGCGGTCAGATTAACTTGCTGGGAACGAACCAT' \
       'TGTCGCCCTCTGCAGCAAGTTAGTTGGCATCATTGGTACTGCCCTTCACTGGTAGCAGCTCCCCCTGTAATATATCCGTGGCCACTATTCAAGGGCTCAAATAGGCGA' \
       'CCCAGAGACCATTATAGGCGGTACAGCGCTGGTAGGTTTGCCTGGGCAGATATCGTTAGCCCCTTCTGCGCGCTATAAGATAGCGAAGGATAATTCTGCGGGACCA' \
       'TGGTCGTCTCCTAACCTCAGGGTGGGATTCCTGGCAGGTGGACCGGGCGCGCATCGAGAGCATTCGGGGTTCCTACCAGCCAGGGAAATCGGGTCGACCACTAGGCAA' \
       'TGAGCGGCTCACACCGATTTTCTTAAGAGACGTAACAAAGCCCGCATTAACGGCTGGAGTGAATCACCGTACGACTACCTAAGCCTCATTGGGATCCACTGTAAACCC' \
       'CTTCGCCGGTGTTGGGTGTCCGCAACGCCTCTGCTTTTTGCGTACAGTCGGCGTGGTGGAGTCCGCGGCCATACTGGCGGTTGGTTTGTAGAACAGTGTAACGACGTG' \
       'TGTCACTGCCCCCCGTAGCTTCTATTGCCCTGTTTGGGAGGTTCTATAGGGGTTACAGAGTAGTTTTAAGTTTTAGCACGACAGCACCAGTATTGCCAGTGACGCCGT' \
       'TGAGGCCGCAAAAGTGATTAACCCCCGTGGGACCGGATACGTTCCCAGCGGCAATCCTTGTCTTACCGCCGGACTGCGGAGCGAAGGGAGAAGTAACCGTGGTAATTA'

dna4 = 'CAGAGCAATGTCTGTTAGATAATCTCTCGTCTGGATAGCGAGAAGTTTCCGGAAGACGATTGTTTCCAACGAAAGGGCTGATAACTACACTCTGTCGCGCTTCTTTCG' \
       'TGTTCGCCAAGGGCACATTGGTTTAAAAGTGATCTCGAGAGACGTTTTCCTGACTTGTTGTGTTATATCAACGTAACTTTTAAGTCATATTTTCTCCCTACCCCAGAC' \
       'TAGACGGGTTCCTTTCATCGTCCACCGAGTTGCTTACGAGCAUGACACTTAGCCGGGGAAAAGTTCGCAATTCCGCGACAGCGTCAGGTGTCAAACAGATCCAAGCGA' \
       'AGGCCGCCGTGTAACGGAGAATTGTGGGCGCAGTCAAATAGCTAATTATTGGGAAAGGCCAAGTGGAGTCCGTCAGCGGAACAGCCTGGGCGGACGCGCTGCCGCTCG' \
       'TTCACCTCGCCTGCCTTCGTGTTGGGGACCGGATACGTTCCCAGCGGCAATCCTTGTCTTACCGCCGGACTGCGGAGCGAAGGGAGAAGTAACCGTGGTAATTAGCGA' \
       'GAGACCGTTGAGGCGCGGGGCGATCCGCCCTTGAGTGGACTCCAAACACATTCGACGAAGGGGTGGGAACATAAGTTAATTGGAGGGTCGGGGAAGTCCCACGCCCGG' \
       'TCCCTACATGATTGCACATAGTTCGTTCACCAACGGGCGATCTTCCTCACACTAGAGGAACGAGTAGTACTCCAGACATTGAGTCAGTTGCAGACCAAGTGGAGGGAA' \
       'CGATTTTTAUGGGCCGCTCAGGTACTAGTGCTAGACCCTACAAACGGCACTGGTGACCCGCTCCCGAGTTTGCGCTGTTACGTGTCCCTTAAAGTATACTTCGATCCT' \
       'AACATCGCGGCCATACGACGCTTAAATATTTCACCAGTTGTGTTTCGCGCAUGGAGTTGTTCTGTGTTATCGGCGAGTCTCCATTGCACGTCATCAACTAAAAACCAC' \
       'GGCCACACAGACATGCCTTGATTCTTCCCGCGACGGTAGGTTTGCCTGGGCAGATATCGTTAGCCCCTTCTGCGCGCTATAAGATAGCGATAGTAGGTTTAACTATCA'

print(dna4.upper())
# why using the \ line extender and not triple-quoted strings?