(FA18-MSBI-0001)

Assignment -2 of Bioinformatics-I (BI5010) 15-10-2018

Task: Write a Python script to find Total number Open Reading Frames (orf) in
Hepatitis C virus complete genome sequence and predict the Gene on the basis of
Orf. Also find the Translated Protein Sequence (CDS) of predicted ORF gene.

Solution:
We use ipython jupyter Notebook for this task. First we import Biopython libraries to calculate
translated protein sequence after orf gene finding. We open the genome file and declare the
orf_finder function, in function we use 2 arguments which are DNA and frame then we define
start and stop codon values, Stored Start Stop Positions in list also declare where to start and
stop. After that we use for loop because we have many base pairs, i:i+3 is used in loop to make
chunks of 3 amino acids which is required. We declared founds orf in dictionary (key, value) and uses if
else condition to make our script more useful, counter is a container that keeps track of how many times
equivalent values of orf are added so basically its used to define orf. Then we use 2nd dictionary to save
our genome sequence and also declare for loop in dict to skip first line (header) and only read original
sequence of fasta file. After that we define frame because our script reading with all 3 reading frames.
Finally we access and view dictionary values through .items() function and print the orf number and
data. We find longest orf with 9084 bp length so we can say that it will be a gene because when
scientists first time discovered orf then they directly said them as a gene but latest discoveries in
genomics proves them wrong. After finding of orf gene, we calculate translated protein sequence by
using .translate () function through Biopython libraries

Script:
# Importing Biopython Libraries

from Bio.Seq import Seq

from Bio import SeqIO
from Bio.Alphabet import IUPAC

# Opening of Genome File

Genome_Seq = open("C:\\Users\\cnn\\Desktop\\MS(BI)\\Bioinformatics 1\\HCV.txt")

#Defining and Declaring of Function

def ORF_Finder(Dna,Frame):

Stop_Codons = ['TGA', 'TAG', 'TAA']

Start_Codon = ['ATG']
Start_Positions = []
Stop_Positions = []
Num_Starts=0
Num_Stops=0
for i in range(Frame-1,len(Dna),3):
Codon=Dna[i:i+3]
if Codon in Start_Codon:
Start_Positions += str(i+1).splitlines()
if Codon in Stop_Codons:
Stop_Positions += str(i+1).splitlines()

for line in Stop_Positions:

Num_Stops += 1

for line in Start_Positions:

Num_Starts += 1

ORFfound = {}

if Num_Stops >=1 and Num_Starts >=1: #First Statment: the number of Stop Codons and Start Codons
are greater than or equal to 1;

ORFs = True
Stop_Before = 0
Start_Before = 0

if Num_Starts > Num_Stops:

Num_Runs = Num_Starts
if Num_Stops > Num_Starts:
Num_Runs = Num_Stops
if Num_Starts == Num_Stops:
Num_Runs = Num_Starts

Position_Stop_Previous = 0
Position_Start_Previous = 0
Counter = 0

for Position_Stop in Stop_Positions:

 Position_Stop = int(Position_Stop.rstrip()) + 2

for Position_Start in Start_Positions:

Position_Start = Position_Start.rstrip()

if int(Position_Start) < int(Position_Stop) and int(Position_Stop) > int(Position_Stop_Previous)

and int(Position_Start) > int(Position_Stop_Previous):

Counter += 1
Name_Orf = "ORF"+str(Counter)
Position_Stop_Previous += int(Position_Stop) - int(Position_Stop_Previous)
Position_Start_Previous += int(Position_Start) - int(Position_Start_Previous)
Size_Orf = int(Position_Stop) - int(Position_Start) + 1

ORFfound[Name_Orf] = Position_Start,Position_Stop,Size_Orf,Frame

else:

pass

else:

ORFs = False

return ORFfound

#FUNCTION END

# READ Sequence FILE AND SAVE Them IN A DICTIONARY

SEQs={}
for Line in Genome_Seq:
Line = Line.rstrip()
if Line[0] == '>':
Dna_Words=Line.split()
Name=Dna_Words[0][1:]
SEQs[Name]= ''
else:
SEQs[Name]= SEQs[Name] + Line
# DEFINE FRAME TO FIND ORF

# if Frame = 1, start from the first position in the sequence

Frame= int(input("Enter Frame Number: "))

# EXECUTE THE ORF_Finder FUNCTION

for i in SEQs.items():
Header= i[0]
seq = i[1]
Orf = ORF_Finder(seq,Frame)
print("\nThe Total ORF Found in Frame" ,Frame, "is : " ,len(Orf) ,'\n\n' )
Orf_gene = seq[339:9423]
Orf_Protein =Seq(Orf_gene)

for i in Orf.items():
Num_Orf = i[0]
Start_Orf = Orf[Num_Orf][0]
Stop_Orf = Orf[Num_Orf][1]
Length_Orf = Orf[Num_Orf][2]
Frame_Orf = Orf[Num_Orf][3]
print(Num_Orf,"starts from",Start_Orf,"bp and stop at",Stop_Orf,"bp , length:",Length_Orf,",
Frame:",Frame_Orf,'\n')
if Length_Orf >= 150:
print(Num_Orf , "in Frame" ,Frame_Orf, "is legimate ORF as it contains more than 150 Base Pairs
in b/w start and stop codon \n")

if Length_Orf >= 1503:

print("\t",Num_Orf , "in Frame" ,Frame_Orf , " would be a predicted gene")

print("\nThe Nucleotide Sequence of predicted ORF Gene:\n" ,Orf_gene ,
"\n\tLength:",len(Orf_gene) )
print("\nThe Translated Protein Sequence(CDS) of predicted ORF gene:
",'\n',Orf_Protein.translate(),"\n\tLength:",len(Orf_Protein.translate()))

Genome_Seq.close() # Closing of Genome File

Result:
Input:

Output:
Enter Frame Number: 1
The Total ORF Found in Frame 1 is : 2

ORF1 starts from 94 bp and stop at 141 bp , length: 48 , Frame: 1

ORF2 starts from 340 bp and stop at 9423 bp , length: 9084 , Frame: 1

ORF2 in Frame 1 is legimate ORF as it contains more than 150 Base Pairs in
b/w start and stop codon

ORF2 in Frame 1 would be a predicted gene

The Nucleotide Sequence of predicted ORF Gene:

ATGAGCACACTTCCTAAACCTCAAAGAAAAACCAAAAGAAAACCCATCCGTCGCCCACAGGACGTCAAGTTCC
CGGGTGGCGGACAGATCGTTGGTGGAGTATACGTGTTGCCGCGCAGGGGCCCACGATTGGGTGTGCGCGCGACG
CGTAAGGCTTCTGAACGGTCACAGCCTCGCGAACGACGACAGCCTATCCCCAAGGCGCGTCGGAGCGAAGGCCG
GTCCTGGGCTCAGCCTGGGTACCCTTGGCCCCTCTATGGTAATGAGGGCTGCGGGTGGGCAGGGTGGCTCCTGT
CCCCCCGCGGCTCCCGTCCATCTTGGGGCCCAAACGACCCCCGGCGAAGATCCCGCAACTTGGGTAAAGTCATC
GATACCCTTACGTGCGGATTCGCCGACCTCATGGGGTACATCCCGCTCGTCGGCGCTCCCGTAGGAGGCGTCGC
AAGAGCCCTCGCGCATGGCGTGAGGGCCCTTGAAGACGGGATAAATTTTGCGACAGGGAACTTGCCCGGTTGCT
CCTTTTCTATCTTCCTTCTTGCTCTACTCTCTTGCTTAATTCATCCAGCAGCCAGTCTAGAGTGGCGGAATACG
TCTGGTCTCTATGTCCTTACCAACGCCCGTTCCAACAGCAGTATAGTGTACGAGGCCGACGACGTTATCCTGCA
CACACCCGGCTGTATACCTTGTGTTCAGACCGGCAACACATCCAAGTGCTGGACCCCAATGACACCCACGGTGG
CAGTTAAGTATGTCGGAGCAACCACCGCTTCGATACGCGGTCATGTGGACCTGTTAGTGGGCGCAGCCACGATG
TGTTCTGCGCTCTACGTGGGTGATGTGTGCGGAGCCGTCTTCCTCGTGGGGCAAGCCTTCACGTTCAGGCCGCG
ACGCCATCAAACGGTCCAGACCTGCAACTGCTCGCTGTACCCAGGCCATCTCACAGGACATCGAATGGCTTGGG
ATATGATGATGAACTGGTCCCCTGCTGTTGGCATGGTGGTGGCGCACATCTTACGCCTACCCCAGACCCTGTTT
GATATAATAGCCGGGGCCCATTGGGGCGTCTTGGCGGGTCTAGCCTACTATACCATGCAGGGCAACTGGGCCAA
GGTCGCAATCATCATGGTTATGTTCTCAGGGGTCGATGCCGTTACGTACATCACTGGGGGCACTGCAGCTCGTG
GGGGCCAAGGGCTGGCTAGCCTAATCGTCCGGGGGCCTGAGCAGCGCCTGGAGCTGATCAACACCCATGGCTCG
TGGCACATCAACAGTACTGTCCTCCACTGCAATGAGTCCATAAACACAGGGTTTATAGCTGGGTTGTTTTATTA
TCATAAGTTCAACTTACTGGATGTCCCGAAGGCTCAGCAGCTGCAAGCCCATCACTTTCTTCAGGCAGGGGTGG
GGCCCCTTGACAGATGCCAACATCCACCGGCCCTTCTGATGACAACCGTACTGCTGGCATACGCACCTAGACCT
TGTGACAGCGTAAAGCAGCACGTGTCTCCGGTCCTGTGTATGCTTCCACACCATCGCCCAGTGGTGGTAGGCAC
TACTGATCCTAAGGGCGCTCCCACCTATAACTGGGGCGAGAATGAGACAGACGTGTTCCTGCTGAATCCCTGCG
GCCTCCTAGTGGTCGGTGGTTTGGGTGGCACGTGGGAGGAACTCCACCGGGGTTTGTCAAGACGTGCGGAGGTT
CCCCCTTGTGACATCTATGGGGGTGGGGGGGAGATCCACCAATGGTTCAGACCTCTTCTGCCCCACCGACTGCT
TCAGGAAACATCCCGAGGCCACATACAGCCGGTGCGGCTCGGGGCCCTGGTTGACACCTCGATGCATGGTCGAC
TATCCATACCGGCTTTGGCATTACCCATGTACAGTCAATTTTACACTGTTCAAGGTGAGGATGTTTGTGGGTGG
GTTTGGCATCGGTTTACCGCCGCTTGCAACTGGACTAGGGGGGAGCGCTGCGATATCGAGGATCGTGACCGCAG
CGAGCAACATCCCCTGCTGCATTCAACAACTGAGCTTGCCATACTGCCTTGCTCTTTCACGCCCATGCCCGCAT
TGTCAACAGGGTTAATACACCTCCACCAAAACATCGTGGATGTCCAATACCTTTATGGCGTTGGATCTGGCATG
GTGGGATGGGCGTTGAAATGGGAATTTGTCATCCTCGTTTTCCTCCTCCTAGCAGATGCACGCGTGTGCGTTGC
CCTTTGGCTGATGCTGATGATATCACAAGCAGAAGCAGCCTGGAGAACTTGTCACGCTGAACGCCGTCTCTGCT
GCCGGGACACATGGTATCGGCTGGTACCTGGTAGCATTTTGCGCGGCGTGGTACGTGCGGGGAAACTCGTCCCG
CTGGTGACCTACAGCCTGACGGGTCTTTGGTCCCTAGCATTGCTCGTCCTTCTACTCCCCCAGCGGGCGTATGC
TTGGTCGGGTGAAGACAGTGCCACCCTCGGCGCTGGGATCTTGGTCCTCTTCGGCTTCTTTACCCTGTCACCTT
GGTATAAGCACTGGATCAGCCGCCTCATGTGGTGGAACCAGTACGCCATATGTAGGTGTGAGTCTGCTCTCCAA
GTATGGGTCCCCCCCCTACTTGCCCGCGGGAGTAGGGACGGTGTTATCCTGCTAACAAGCCTGCTTTATCCATC
ATTAGTTTTTGACATCGCTAAGCTGCTGATAGCCGTAATAGGCCCATTATATCTAATACAGGCCGCCATCACTA
CTACCCCCTACTTTGTGCGTGCGCATGTTCTGGTCCGCCTTTGCATGTTCGTGCGCTCCGTGACGGGGGGAAAG
TACTTCCAGATGGCCATACTGAGCGTCGGCAGATGGTTTAACACCTACCTATATGACCACCTTGCACCGATGCA
ACACTGGGCCGCAGCAGGCCTCAAAGACCTGGCAGTAGCCACTGAACCTGTAATATTCAGTCCCATGGAAATCA
AGGTCATCACTTGGGGCGCGGACACGGCAGCTTGCGGAGATATCCTATGCGGGCTGCCCGTCTCTGCACGATTA
GGCCGTGAGGTGTTGTTGGGACCTGCTGATGACTATCGGGAGATGGGCTGGCGTCTGTTGGCCCCGATTACAGC
ATACGCCCAGCAAACTAGGCGTCTTTTTGGGACTATTGTGACCAGCTTGACTGGCAGGGACAAGAACGTGGTGG
CCGGCGAAGTGCAGGTGCTTTCTACGGCTACCCAGACCTTCCTAGGTACAACATTGGGAGGGGTTATGTGGACT
GTTTACCATGGAGCAGGTTCGAGAACACTTGCGGGCGTCAAACATCCTGCGCTCCAAATGTACACAAATGTAGA
TCAGGACCTCGTTGGATGGCCAGCTCCTCCGGGGGCTAAGTCTCTTGAACCGTGCACCTGCGGGTCTGCGGACT
TGTACTTGGTTACCCGCGAAGCTGATGTCATCCCTGCTAGACGCAGGGGGGACTCCACAGCGAGCTTGCTCAGT
CCTAGGCCTCTCGCCTGTCTCAAAGGTTCCTCTGGAGGTCCTGTTATGTGCCCTTCGGGCCACGTAGCGGGGAT
CTTTAGGGCTGCTGTGTGCACCAGAGGTGTAGCAAAAGCCCTACAGTTCATACCAGTGGAAACCCTTAGCACAC
AGGCTAGGTCTCCATCCTTTTCTGACAATTCAACTCCTCCTGCTGTTCCACAGAGCTATCAAGTAGGGTACCTT
CATGCCCCGACCGGCAGCGGTAAGAGCACAAAGGTCCCGGCCGCTTATGTAGCACAAGGATATAATGTTCTCGT
GTTGAATCCATCAGTGGCGGCCACACTAGGCTTCGGCTCTTTCATGTCGCGAGCTTATGGGATCGACCCCAACA
TCCGCACCGGGAACGGCACGGTTACAACTGGTGCTAATCTGACCTATTCCACCTATGGTAAGTTTCTCGCGGAC
GGGGGTTGCTCGGGGGGAGCATATGATGTGATTATCTGTGATGAGTGTCATGCCCAAGACTCTACTAGCATACT
GGGTATAGGCACGGTCCTAGATCAGGCTGAAACGGCTGGGGTGAGGCTGACGGTTTTAGCAACAGCAACTCCCC
CAGGCAGCATCATTGGGCCCCATTCTAACCTCAAAGAAGTGGCCCTTGGTTCTGAGGGGGAGATCCCTTTCTTC
GGCAAGGCCATACCGCTAGCCCTGCTAAGGGGGAAAGGCACCTTATTTTTTTCCATTCCAAGAAAAAATGTGAT
GAGATGGCATCCAAACTCAGAGGCATGGGGCTCAACGCTGAAGGAGTACTACAGGGGTCTTGATGTGTCCGTCA
TACCAACATCAGGAGACGTTGTAGTTTGCGCTACTGACGCCCTCATGACTGGATTCACCGGAGACTTCGACTCT
GTCATAGATTGCAACGTGGCTGTTGAACAGTACGTTGATTTCAGCTTGGACCCCACCTTTTCCATTGAGACTCG
CACTGCTCCCCAAGACGCGGTTTCCCGCAGTCAACGTCGTGGCCGTACGGGCCGAGGTAGACTCGGCACGTACC
GATATGTCACCCCCGGTGAAAGACCGTCTGGGATGTTTGACTCGGCTGTTCTCTGTGAGTGCTATGACGCGGGC
TGCTCGTGGTACGACTTGCAGCCCGCCGAGACCACAGTCAGACTAAGAGCTTACTTGTCCACGCCGGGGTTACC
TGTCTGCCAAGACCACTTGGAATTTTGGGAGAGCGTCTTCACTGGACTAACTCACATAGATGCCCACTTTCTAT
CACAGACCAAGCAGCAGGGACTCAACTTCCCATACCTAGCTGCCTACCAAGCCACTGTGTGCGCTCGCGCGCAA
GCTCCTCCCCCAAGTTGGGACGAGACATGGAAGTGTCTCGTGCGGCTTAAGCCAACACTACATGGACCTACACC
CCTTCGATATCGGCCGGGGCCTGTCCAAAATGAAACCTGCTTGACACACCCCATCACAAAATACCTCATGGCAT
GCATGTCAGCCGATCTGGAAGTAACCACCAGCACCTGGAGCACCTGGGTGTTGCTCGGAGGGGTCCTCGCGGCC
CTGGCAGCCTACTGCTTGTCGGTCGGCTGCGTAGTCATTGTGGGCCACATTGAGCTGGGGGGCAAGCCGGCGCT
CGTTCCTGACAAAGAAGTGTTGTATCAACAATACGATGAGATGGAGGAGTGCTCACAAGCTGCCCCATATATCG
AACAAGCTCAAGTAATAGCCCACCAGTTCAAGGAAAAAGTCCTTGGATTGCTACAGCGAGCTACCCAACAACAA
GCTGTCATTGAGCCCATAGTAGTTACCAACTGGCAAAAGCTTGAGGCCTTCTGGCACAAGCACATGTGGAACTT
TGTGAGTGGGATTCAGTACCTAGCAGGTCTCTCCACTTTGCCCGGCAACCCCGCTGTGGCGTCTCTTATGGCGT
TCGCTGCTTCAGTCACCAGTCCCCTGACGACCAATCAAACTATGTTTTTTAACATACTCGGGGGATGGGTTGCT
ACTCATTTGGCAGGGCCCCAGAGCTCTTCCGCATTCGTGGTAAGCGGCTTGGCCGGCGCTGCCATAGGGGGCAT
AGGCCTGGGCAGGGTCTTACTTGACATCCTGGCAGGATACGGAGCTGGTGTCTCAGGCGCCTTGGTGGCTTTCA
AAATCATGGGGGGGGAACTCCCCAATGCCGAGGACGTGGTCAATCTGTTGCCCGCCATACTATCTCCGGGTGCT
CTCGTCGTCGGGGTGATATGCGCTGCCCTACTACGTCGGCACGTGGGACCTGGGGAGGGAGCGGTACAGTGGAT
GAACAGGCTCATCGCGTTCGCATCCCGGGGCAACCACGTCTCACCGACGCACTATGTTCCCGAGAGCGATGCTG
CGGCAAGGGTCACCGCATTGCTGAGTTCTCTAACTGTCACAAGTCTGCTCCGGCGGTTACACCAGTGGATCAAT
GAAGACTACCCAAGCCCTTGTAGCGACGATTGGCTACGTACCATCTGGGACTGGGTCTGCATGGTGTTGCTCGA
CTTCAAGACATGGCTGTCTGCTAAGATCATGCCATTGCTCCCTGGGTTGCCCTTCATTTCCTGTCAAAAGGGAT
ATAAGGGCGTTTGGCAGGGGGACGGCGTGGTGTCCACTCGCTGTCCTTGCGGAGCAGTGATAACCGGTCATGTG
AAGAACGGGTCCATGCGGCTTGCAGGACCACGTACATGTGCTAACATGTGGCACGGCACCTTCCCCATCAACGA
GTACACCACCGGACCCAGCACACCTTGCCCATCACCCAACTACACTCGTGCACTGTGGCGCGTGGCTGCCAACA
GCTACGTCGAAGTGCGACGGGTGGGAGACTTCCACTACATCACGGGGGCCACAGAAGATGAGCTCAAGTGTCCG
TGCCAAGTGCCGGCTGCTGAGTTCTTTACTGAAGTGGATGGGGTGAGACTTCACCGTTACGCCCCTCCATGCAG
GCCCCTGTTGAGGGATGAGATCACTTTCGTAGTAGGGCTGAATTCTTACGCGATAGGATCCCAACTCCCTTGTG
AGCCCGAACCGGACGTCTCTGTGCTGACCTCGATGTTGAGAGACCCTTCCCATATCACCGCCGAGACGGCAGCG
CGCCGCCTTGCACGCGGGTCCCCTCCATCAGAGGCAAGCTCATCCGCCAGTCAACTATCGGCTCCATCGTTGAA
GGCCACTTGCCAAACGCATAGGCCTCATCCCGACGCGAGCTGGTGGACGCCAACTTGTGTTTGGCGACAAGAGA
TGGGCAGCAACATCACACGGGTAGAGTCCGAAACAAAGGTTGTGATTCTTGACTCATTCGAACCTCTGAGGGCC
GAGACTGATGACACCGAGCTCTCGGTAGCAGCAGAGTGTTTCAAGAAACCTCCCAAGTATCCTCCAGCCCTCCC
TATCTGGGCTAGGCCAGACTACAACCCTCCACTGTTGGATCGTTGGAAATCACCGGATTATGAACCACCAATTG
TTCATGGGTGCGCCTTACCACCACAGGGTACTCCACCGGTGCCTCCCCCTCGGAGGAAAAGAACAATCCAGCTG
GACGGCTCCAATGTGTCCGCGGCGCTAGCTGCGCTAGCGGAAAAATCATTCCCGGCCTCAAAACCGTTGGAAGC
GGGTAGCTCATCCTCAGGGGTCGATACACAGTCCAGCACTACTTCCAAGGTGCCTCCCTCTTCGGAGAGAGAGT
CCGACACAGAATCGTGCTCGTCCATGCCTCCTCTCGAGGGGGAGCCGGGCGATCCAGACTTGAGTTGCGACTCT
TGGTCCACTGTTAGTGACAGCGAGGAGCAGAGCGTGGTCTGCTGCTCTATGTCGTATTCTTGGACCGACGCCCT
GATAACACCATGTAGTGCTGAGGGAGAGAACTGCCCATCAGCCCACTCAGCAATCTTGGAGAGACATCACAACC
TAATCTATTCAACGTCGTCTAGAATCGCTTCTCAACGTCAGAAGAAGGTCACCTTCGACAGGCTGCAGGTGCTC
GACGACCATTACAAAACTGCATTAAAGGAGATAAAGGAGCGAGCGTCAAGGGTAAAGGCTCGCATGCTCACCAT
CGAGGAAGCGTGCGCGCTCGTCCCTCCTCACTCTGCTCGGTCAAAGTTCGGGTATAGTGCGAAGGACGCTCGCT
CCCTGTCCAGCAAGGCCATTAACCAGATCCGCTCCGTCTGGGAGGACTTGCTGGAAGACACCACAACTCCAATT
CCAACCACCATCATGGCGAAGAGCGAGGTTTTTTGTGTGGATCCTACTAAAGGAGGCCGTTTTTTGCTCGTCTC
ATTGTCTACCCTGACCTGGGGGTGCGCATCTGTGAGAACGTGCCCTATATGGCGTGATACAGAAGTGGGGAGTG
GGGACGATGGGTCCTGCCTATGGATTCCAATACTCGCCTCAACAGCGGGTCGAACGTCTGCTGAAGATGTGGAC
CTCAAAGAAAGCCCAGTTGGGGTTCTCGTATGGTACCCGCTGCTTTGGCTCGACTGCCACTGGACAGGACATCA
GGGTGGAAGAGGAGATATACCAATGCTGGAGCCTTGGACCGGAGGCCAGGAAAGTGATCTCCTCCCTCACGGAG
CGGCTTTACTGCGGAGGCCCTATGTTCAACAGCAAGGGGGCCCAGTGTGGTTATCGCCGTTGCCGTGCCAGTGG
AGTTCTGCCTACCAGCTTCGGCAACACGATCACTTGTTACATCAAGGCCACAGCGGCTGCAAAGGCCGCAAACC
TCCGGAAGCCTGGCTTCTTGTTTGGGGAGGATGGATCCTGGTCGTATTACCTGAGGACCGAATGGGGTTCGAAT
GGAGATACGGGCAGTCCTGGGAGAGCCTTCACCGGAGGCTATGGACCAGGTATTTCTTGCTTCCACCCGGAGAT
GGCCCCCACAGGCCAACCCTACGACCTTTGGGCTCATTACATCTGGCTCCTCCAACGTCTCCGTGGCGCGGGAC
GATACGGGGAAGAGGTATTATTACCTCACTCGTGGTGCCACCACCCCCCTGGCCCGTGCTGCTTGGGAGACAGC
TCGTCACACTCCAGTTACCTCCTGGCTGGGGAACATCATCATGTACGCGCCTACTATTTGGGTGCGCATGGTGG
TGGTGGCACACTTTTTCTCCATACTCCAATCCCAGGAGATACTTGGTCGCCCCCTTGGCTTTGGAATGTACGGG
GCCACTTACTCTGTCACTCCGCTGGATTTACCAGCAATCATTGGAAGACTCCATGGTCTACGCGCGTTTACGCT
CCATATTTACTCTCCAGCAGAGCTCAATACGGTCGCGGGGACACTCAGGAAGCTTGTGCCCCCCCCTACGAGCT
TGGAGACATCGGGCACGAGCAGTGCGCGCTATGCTTATCGCCCAGGGAGGGAAGGCCAGGATTTGTGGGCTTTA
TCACTTCAATTGGGCGGTACGCACCAAGACCACCCTCACTCCACTGCCAGCCGCTGGCCAGTTGGATTTATCCA
TCTGGTTTACGGTTGGTGTCGGCGGGAACGACATTCTCGCAGCGTGTCACGCGCCCGAACCCGCCATTTGCTGC
TTTGCCTACTCCCTACTAACAGTAGGGGTAGGCATCTTTCTCTTGCCAGCTCGATGA
Length: 9084

The Translated Protein Sequence (CDS) of predicted ORF gene:

MSTLPKPQRKTKRKPIRRPQDVKFPGGGQIVGGVYVLPRRGPRLGVRATRKASERSQPRERRQPIPKARRSEG
RSWAQPGYPWPLYGNEGCGWAGWLLSPRGSRPSWGPNDPRRRSRNLGKVIDTLTCGFADLMGYIPLVGAPVGGV
ARALAHGVRALEDGINFATGNLPGCSFSIFLLALLSCLIHPAASLEWRNTSGLYVLTNARSNSSIVYEADDVIL
HTPGCIPCVQTGNTSKCWTPMTPTVAVKYVGATTASIRGHVDLLVGAATMCSALYVGDVCGAVFLVGQAFTFRP
RRHQTVQTCNCSLYPGHLTGHRMAWDMMMNWSPAVGMVVAHILRLPQTLFDIIAGAHWGVLAGLAYYTMQGNWA
KVAIIMVMFSGVDAVTYITGGTAARGGQGLASLIVRGPEQRLELINTHGSWHINSTVLHCNESINTGFIAGLFY
YHKFNLLDVPKAQQLQAHHFLQAGVGPLDRCQHPPALLMTTVLLAYAPRPCDSVKQHVSPVLCMLPHHRPVVVG
TTDPKGAPTYNWGENETDVFLLNPCGLLVVGGLGGTWEELHRGLSRRAEVPPCDIYGGGGEIHQWFRPLLPHRL
LQETSRGHIQPVRLGALVDTSMHGRLSIPALALPMYSQFYTVQGEDVCGWVWHRFTAACNWTRGERCDIEDRDR
SEQHPLLHSTTELAILPCSFTPMPALSTGLIHLHQNIVDVQYLYGVGSGMVGWALKWEFVILVFLLLADARVCV
ALWLMLMISQAEAAWRTCHAERRLCCRDTWYRLVPGSILRGVVRAGKLVPLVTYSLTGLWSLALLVLLLPQRAY
AWSGEDSATLGAGILVLFGFFTLSPWYKHWISRLMWWNQYAICRCESALQVWVPPLLARGSRDGVILLTSLLYP
SLVFDIAKLLIAVIGPLYLIQAAITTTPYFVRAHVLVRLCMFVRSVTGGKYFQMAILSVGRWFNTYLYDHLAPM
QHWAAAGLKDLAVATEPVIFSPMEIKVITWGADTAACGDILCGLPVSARLGREVLLGPADDYREMGWRLLAPIT
AYAQQTRRLFGTIVTSLTGRDKNVVAGEVQVLSTATQTFLGTTLGGVMWTVYHGAGSRTLAGVKHPALQMYTNV
DQDLVGWPAPPGAKSLEPCTCGSADLYLVTREADVIPARRRGDSTASLLSPRPLACLKGSSGGPVMCPSGHVAG
IFRAAVCTRGVAKALQFIPVETLSTQARSPSFSDNSTPPAVPQSYQVGYLHAPTGSGKSTKVPAAYVAQGYNVL
VLNPSVAATLGFGSFMSRAYGIDPNIRTGNGTVTTGANLTYSTYGKFLADGGCSGGAYDVIICDECHAQDSTSI
LGIGTVLDQAETAGVRLTVLATATPPGSIIGPHSNLKEVALGSEGEIPFFGKAIPLALLRGKGTLFFSIPRKNV
MRWHPNSEAWGSTLKEYYRGLDVSVIPTSGDVVVCATDALMTGFTGDFDSVIDCNVAVEQYVDFSLDPTFSIET
RTAPQDAVSRSQRRGRTGRGRLGTYRYVTPGERPSGMFDSAVLCECYDAGCSWYDLQPAETTVRLRAYLSTPGL
PVCQDHLEFWESVFTGLTHIDAHFLSQTKQQGLNFPYLAAYQATVCARAQAPPPSWDETWKCLVRLKPTLHGPT
PLRYRPGPVQNETCLTHPITKYLMACMSADLEVTTSTWSTWVLLGGVLAALAAYCLSVGCVVIVGHIELGGKPA
LVPDKEVLYQQYDEMEECSQAAPYIEQAQVIAHQFKEKVLGLLQRATQQQAVIEPIVVTNWQKLEAFWHKHMWN
FVSGIQYLAGLSTLPGNPAVASLMAFAASVTSPLTTNQTMFFNILGGWVATHLAGPQSSSAFVVSGLAGAAIGG
IGLGRVLLDILAGYGAGVSGALVAFKIMGGELPNAEDVVNLLPAILSPGALVVGVICAALLRRHVGPGEGAVQW
MNRLIAFASRGNHVSPTHYVPESDAAARVTALLSSLTVTSLLRRLHQWINEDYPSPCSDDWLRTIWDWVCMVLL
DFKTWLSAKIMPLLPGLPFISCQKGYKGVWQGDGVVSTRCPCGAVITGHVKNGSMRLAGPRTCANMWHGTFPIN
EYTTGPSTPCPSPNYTRALWRVAANSYVEVRRVGDFHYITGATEDELKCPCQVPAAEFFTEVDGVRLHRYAPPC
RPLLRDEITFVVGLNSYAIGSQLPCEPEPDVSVLTSMLRDPSHITAETAARRLARGSPPSEASSSASQLSAPSL
KATCQTHRPHPDASWWTPTCVWRQEMGSNITRVESETKVVILDSFEPLRAETDDTELSVAAECFKKPPKYPPAL
PIWARPDYNPPLLDRWKSPDYEPPIVHGCALPPQGTPPVPPPRRKRTIQLDGSNVSAALAALAEKSFPASKPLE
AGSSSSGVDTQSSTTSKVPPSSERESDTESCSSMPPLEGEPGDPDLSCDSWSTVSDSEEQSVVCCSMSYSWTDA
LITPCSAEGENCPSAHSAILERHHNLIYSTSSRIASQRQKKVTFDRLQVLDDHYKTALKEIKERASRVKARMLT
IEEACALVPPHSARSKFGYSAKDARSLSSKAINQIRSVWEDLLEDTTTPIPTTIMAKSEVFCVDPTKGGRFLLV
SLSTLTWGCASVRTCPIWRDTEVGSGDDGSCLWIPILASTAGRTSAEDVDLKESPVGVLVWYPLLWLDCHWTGH
QGGRGDIPMLEPWTGGQESDLLPHGAALLRRPYVQQQGGPVWLSPLPCQWSSAYQLRQHDHLLHQGHSGCKGRK
PPEAWLLVWGGWILVVLPEDRMGFEWRYGQSWESLHRRLWTRYFLLPPGDGPHRPTLRPLGSLHLAPPTSPWRG
TIRGRGIITSLVVPPPPWPVLLGRQLVTLQLPPGWGTSSCTRLLFGCAWWWWHTFSPYSNPRRYLVAPLALECT
GPLTLSLRWIYQQSLEDSMVYARLRSIFTLQQSSIRSRGHSGSLCPPLRAWRHRARAVRAMLIAQGGKARICGL
YHFNWAVRTKTTLTPLPAAGQLDLSIWFTVGVGGNDILAACHAPEPAICCFAYSLLTVGVGIFLLPAR*
Length: 3028

Note:
This Script only works for Fast Sequence Files which contains header in
first line. If we open and read .txt file with no header in first line then the
output gives error. To access those files we have to change the code in for
loop of 2nd dictionary which contains DNA sequence and all script except
2nd dictionary remains same