6/5/2021 Čas 1

Primer učitavanja sekvence iz fajla i translacije

In [1]:

from Bio.Seq import Seq

import Bio.SeqIO as SeqIO

from Bio.Alphabet import generic_dna, generic_protein

In [2]:

# Ucitavanje sekvence HBB proteina pacijenta iz fajla.

# Data je nukleotidna sekvenca koja kodira HBB protein

sick_patient_sequence = SeqIO.read('HBS.fasta', 'fasta')

In [3]:

# Ceo rekord

print(sick_patient_sequence)

# Sekvenca

print(sick_patient_sequence.seq)

ID: Sick

Name: Sick

Description: Sick patient HBB

Number of features: 0

Seq('ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGG...CAA', Single
LetterAlphabet())

ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGTGGAG
AAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCT
GGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCA
ACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTC
AAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCT
GGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATC
AGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAAGCTCGCTTTCTTGCTGTCCAATTT
CTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGG
ATTCTGCCTAATAAAAAACATTTATTTTCATTGCAA

In [4]:

# Proteinska sekvenca zdravog HBB proteina

hbb = Seq('MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGL
AHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH', generic_dna)

print(hbb)

MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSD
GLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

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In [5]:

# translated_sick = sick_patient_sequence.seq[0:].translate() # okvir 1

# translated_sick = sick_patient_sequence.seq[1:].translate() # okvir 2

# Translirana DNK (posredstvom mRNK) u proteinsku sekvencu od treceg okvira

translated_sick = sick_patient_sequence.seq[2:].translate()

print(translated_sick)

ICF*HNCVH*QPQTDTMVHLTPVEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN
PKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQ
KVVAGVANALAHKYH*ARFLAVQFLLKVPLFPKSNY*TGGYYEGP*ASGFCLIKNIYFHC

/usr/local/lib/python3.7/site-packages/Bio/Seq.py:2859: BiopythonWarning:
Partial codon, len(sequence) not a multiple of three. Explicitly trim the
sequence or add trailing N before translation. This may become an error in
future.

BiopythonWarning,

In [6]:

# Prva pojava Metionina (startne aminokiseline)

translated_sick.find('M')

Out[6]:

16

In [7]:

start_codon = translated_sick.find('M')

sliced_sequence = translated_sick[start_codon:]

# Pronalazenje prvog stop kodona od M

stop_codon = sliced_sequence.find('*')
sliced_sequence = sliced_sequence[:stop_codon]

print(sliced_sequence)

MVHLTPVEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSD
GLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

In [8]:

print(hbb)

print()

print(sliced_sequence)

MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSD
GLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

MVHLTPVEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSD
GLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

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In [9]:

# Pronalazenje razlika izmedju proteinskih sekvenci zdravog i bolesnog HBB

# U pitanju je srpasta anemija kod koje se, usled mutacije jednog nukleotida

# na 6. poziciji (7. ako se broji od 0) aminokiselina Glutamat (E) menja Valinom (V)

for i in range(len(hbb)):

if hbb[i] != sliced_sequence[i]:

print(f'Pos: {i}, {hbb[i]}->{sliced_sequence[i]}')

Pos: 6, E->V

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