def indentifyMutationInformation(record, reference_sequence_informations):
# If same pattern as reference sequence
if record["pattern"] == reference_sequence_informations["pattern"]:
# Save the information associated to the reference pattern
return [
record["id"], reference_sequence_informations["organisme"],
record["type"], reference_sequence_informations["pattern"], None,
reference_sequence_informations["gene"], None, record["position"]
]
# If different pattern as reference sequence
else:
# If a pattern variation has been identified
if record["pattern"] != None:
# Get the position of the initial pattern
start = reference_sequence_informations["position_gene_sequence"]
end = reference_sequence_informations[
"position_gene_sequence"] + len(record["pattern"])
# Generate the mutated sequence
mutated_squence = ""
mutated_squence = mutated_squence + reference_sequence_informations[
"nucleotide_sequence"][0:start]
mutated_squence = mutated_squence + record["pattern"].replace(
"-", "")
mutated_squence = mutated_squence + reference_sequence_informations[
"nucleotide_sequence"][end:]
rna_sequence = transcribe(mutated_squence)
aa_sequence = str(rna_sequence.translate())
# Get the mutation
mutations = getMutation(
reference_sequence_informations["amino_acid_sequence"],
aa_sequence)
if len(mutations) <= 5:
return [
record["id"], reference_sequence_informations["organisme"],
record["type"], reference_sequence_informations["pattern"],
record["pattern"], reference_sequence_informations["gene"],
mutations, record["position"]
]
else:
return [
record["id"], reference_sequence_informations["organisme"],
record["type"], reference_sequence_informations["pattern"],
"Not identified", "Not identified", "Not identified",
"Not identified"
]
# If unidentified pattern
else:
return [
record["id"], reference_sequence_informations["organisme"],
record["type"], reference_sequence_informations["pattern"],
"Not identified", "Not identified", "Not identified",
"Not identified"
]
def translator(path_to_fasta, codons_table):
fasta_file = open(path_to_fasta, 'r')
seq_records = parse(fasta_file, 'fasta')
for seq_record in seq_records:
dna_seq = seq_record.seq
rna_seq = transcribe(dna_seq)
protein_seq = translate(rna_seq, codons_table)
yield protein_seq
fasta_file.close()
def directStringSeq():
my_string = "GCTGTTATGGGTCGTTGGAAGGGTGGTCGTGCTGCTGGTTAG"
Compl = complement(my_string)
reCompl = reverse_complement(my_string)
transc = transcribe(my_string)
bTransc = back_transcribe(my_string)
transl = translate(my_string)
print('my_string = ', my_string)
print('Compl = ', Compl)
print('reCompl = ', reCompl)
print('transc = ', transc)
print('bTransc = ', bTransc)
print('transl = ', transl)
def TransPageView(request):
if request.method == "POST":
xseq = request.POST.get('sequence')
my_dna = validateseq(xseq)
if my_dna == "error":
messages.info(request, 'Invalid DNA sequence')
return render(request, "transcription.html")
else:
transseq = transcribe(my_dna[0])
return render(request, "transcription.html",{
'seq':my_dna[0] ,
'transseq':transseq ,
})
else:
return render(request,"transcription.html")
def TranslatePageView(request):
if request.method == 'POST':
xseq = request.POST.get('sequence')
xoption = request.POST.get('gencode')
my_rna = validaterna(xseq)
if my_rna == "error":
my_dna = validateseq(xseq)
if my_dna == "error":
messages.info(request,'Invalid Sequence')
return render(request, "translate_base.html")
else:
my_new_rna = transcribe(my_dna[0])
my_translation = six_frame_translations(my_new_rna,xoption)
return render( request, "translate_result.html",{
'trans_one':my_translation[1] ,
'trans_two':my_translation[2] ,
'trans_three':my_translation[3] ,
'my_seq':my_translation[4] ,
'my_seq_comp':my_translation[5] ,
'comp_one':my_translation[6] ,
'comp_two':my_translation[7] ,
'comp_three':my_translation[8] ,
})
else:
my_translation = six_frame_translations(my_rna,xoption)
return render( request, "translate_result.html",{
'trans_one':my_translation[1] ,
'trans_two':my_translation[2] ,
'trans_three':my_translation[3] ,
'my_seq':my_translation[4] ,
'my_seq_comp':my_translation[5] ,
'comp_one':my_translation[6] ,
'comp_two':my_translation[7] ,
'comp_three':my_translation[8] ,
})
else:
return render( request, "translate_base.html")
def apply_operation():
"""Do the selected operation."""
codon_table = codon_list.get(codon_list.curselection())
print(f"Code: {codon_table}")
seq = "".join(input_text.get(1.0, tk.END).split())
print(f"Input sequence: {seq}")
operation = transform_var.get()
print(f"Operation: {operation}")
if operation == "transcribe":
result = transcribe(seq)
elif operation == "translate":
result = translate(seq, table=codon_table, to_stop=True)
elif operation == "back transcribe":
result = back_transcribe(seq)
else:
result = ""
output_text.delete(1.0, tk.END)
output_text.insert(tk.END, result)
print(f"Result: {result}")
def apply_operation():
"""Do the selected operation."""
codon_table = codon_list.get(codon_list.curselection())
print('Code: {}'.format(codon_table))
seq = ''.join(input_text.get(1.0, tk.END).split())
print('Input sequence: {}'.format(seq))
operation = transform_var.get()
print('Operation: {}'.format(operation))
if operation == 'transcribe':
result = transcribe(seq)
elif operation == 'translate':
result = translate(seq, table=codon_table, to_stop=True)
elif operation == 'back transcribe':
result = back_transcribe(seq)
else:
result = ''
output_text.delete(1.0, tk.END)
output_text.insert(tk.END, result)
print('Result: {}'.format(result))
return
def apply_operation():
"""Do the selected operation."""
codon_table = codon_list.get(codon_list.curselection())
print('Code: {}'.format(codon_table))
seq = ''.join(input_text.get(1.0, tk.END).split())
print('Input sequence: {}'.format(seq))
operation = transform_var.get()
print('Operation: {}'.format(operation))
if operation == 'transcribe':
result = transcribe(seq)
elif operation == 'translate':
result = translate(seq, table=codon_table, to_stop=True)
elif operation == 'back transcribe':
result = back_transcribe(seq)
else:
result = ''
output_text.delete(1.0, tk.END)
output_text.insert(tk.END, result)
print('Result: {}'.format(result))
return
from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate my_string = "GCTGTTATGGGTCGTTGGAAGGGTGGTCGTGCTGCTGGTTAG" print(reverse_complement(my_string)) print(transcribe(my_string)) print(back_transcribe(my_string)) print(translate(my_string))
print unk, len(unk), type(unk)
unkDNA = UnknownSeq(20, alphabet=IUPAC.ambiguous_dna)
print unkDNA # N = any base
unkProt = UnknownSeq(10, alphabet=IUPAC.protein)
print unkProt # X = any aminoacid
print unkDNA.complement(), unkDNA.reverse_complement()
print unkDNA.transcribe(), unkDNA.translate()
unkProt = unkDNA.translate()
print unkProt, len(unkProt)
#Directly on strings
from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate
noseq = 'GCTGTTATGGGTCGTTGGAAGGGTGGTCGTGCTGCTGGTTAG'
print reverse_complement(noseq) # these functions
print transcribe(noseq) # receive either strings
print back_transcribe(noseq) # Seq, MutableSeq, UnknownSeq
print translate(noseq)
#SeqRecord object
#.seq A Seq object
#.id a string ID identifier of the sequence
#.name a string common name for the sequence
#.description a string readable description or complete name
#.letter_annotations a dictionary of adittional info about the letters in the sequence.
# The values for the keys are (list, tuple, string) with the same length of the sequence.
#.annotations a dictionary of additional info about the sequence
#.features a list of SeqFeature objects
#.dbxrefs a list of string DB cross-references
from Bio.SeqRecord import SeqRecord
seq = Seq('GATC')
from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate #질문있는데 이걸 꼭 이렇게 불러야겠니 insulin = "GCATTCTGAGGCATTCTCTAACAGGTTCTCGACCCTCCGCCATGGCCCCGTGGATGCATCTCCTCACCGTGCTGGCCCTGCTGGCCCTCTGGGGACCCAACTCTGTTCAGGCCTATTCCAGCCAGCACCTGTGCGGCTCCAACCTAGTGGAGGCACTGTACATGACATGTGGACGGAGTGGCTTCTATAGACCCCACGACCGCCGAGAGCTGGAGGACCTCCAGGTGGAGCAGGCAGAACTGGGTCTGGAGGCAGGCGGCCTGCAGCCTTCGGCCCTGGAGATGATTCTGCAGAAGCGCGGCATTGTGGATCAGTGCTGTAATAACATTTGCACATTTAACCAGCTGCAGAACTACTGCAATGTCCCTTAGACACCTGCCTTGGGCCTGGCCTGCTGCTCTGCCCTGGCAACCAATAAACCCCTTGAATGAG" #Wrap 알아서 켜주면 안되냐고... insulin_rc = reverse_complement(insulin) insulin_mrna = transcribe(insulin) insulin_prot = translate(insulin) # 순서대로 reverse complement/전사/번역 print(insulin_rc) print(insulin_mrna) print(insulin_prot)
# sequence complement (only if alphabet allows complement)
my_seq.complement()
# reverse complement (only if alphabet allows complement)
my_seq.reverse_complement()
# transcribe RNA (DNA -> mRNA)
#The actual biological transcription process works from the template strand, doing a reverse complement
#(TCAG → CUGA) to give the mRNA. However, in Biopython and bioinformatics in general, we typically
#work directly with the coding strand because this means we can get the mRNA sequence just by switching
#T → U.
from Bio.Seq import transcribe
# just changes T with U from the coding strand (5' -> 3')
messenger_rna = transcribe(coding_dna)
# if we want to transcribe from the template strand (3' -> 5'):
transcribe(template_dna.reverse_complement())
# transcribing back to DNA:
from Bio.Seq import Seq, back_transcribe
back_transcribe(messenger_rna) # just changes U -> T and gives the coding strand
# 3.8 Translation (mRNA -> Protein)
# Uses standard genetic code
from Bio.Seq import Seq, translate
from Bio.Alphabet import IUPAC
messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG", IUPAC.unambiguous_rna)
coding_dna.transcribe()#T→U
coding_dna.reverse_complement().transcribe()#true_transcribe
coding_dna.translate(to_stop=True,cds=True)#RNA和DNA都可以直接翻译,table参数可以选择密码子表
from Bio.Data import CodonTable
standard_table=CodonTable.unambiguous_dna_by_id[1]
mito_table = CodonTable.unambiguous_dna_by_name["Vertebrate Mitochondrial"]
standard_table = CodonTable.unambiguous_dna_by_name["Standard"]
mito_table = CodonTable.unambiguous_dna_by_id[2]
from Bio.Seq import MutableSeq
mutable_seq = MutableSeq("GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA", IUPAC.unambiguous_dna)
##或者
mutable_seq = my_seq.tomutable()
mutable_seq[5] = "C"
mutable_seq.remove("T")
mutable_seq.reverse()
new_seq=mutable_seq.toseq()
from Bio.Seq import UnknownSeq
unk_dna=UnknownSeq(20,alphabet=IUPAC.ambiguous_dna)
from Bio.Seq import reverse_complement,transcribe,back_transcribe,translate
my_string = "GCTGTTATGGGTCGTTGGAAGGGTGGTCGTGCTGCTGGTTAG"
reverse_complement(my_string)
transcribe(my_string)
back_transcribe(my_string)
translate(my_string)
def get_info(seq):
return GC(seq), transcribe(seq), translate(seq)
# sequence complement (only if alphabet allows complement)
my_seq.complement()
# reverse complement (only if alphabet allows complement)
my_seq.reverse_complement()
# transcribe RNA (DNA -> mRNA)
#The actual biological transcription process works from the template strand, doing a reverse complement
#(TCAG → CUGA) to give the mRNA. However, in Biopython and bioinformatics in general, we typically
#work directly with the coding strand because this means we can get the mRNA sequence just by switching
#T → U.
from Bio.Seq import transcribe
# just changes T with U from the coding strand (5' -> 3')
messenger_rna = transcribe(coding_dna)
# if we want to transcribe from the template strand (3' -> 5'):
transcribe(template_dna.reverse_complement())
# transcribing back to DNA:
from Bio.Seq import Seq, back_transcribe
back_transcribe(
messenger_rna) # just changes U -> T and gives the coding strand
# 3.8 Translation (mRNA -> Protein)
# Uses standard genetic code
from Bio.Seq import Seq, translate
from Bio.Alphabet import IUPAC
messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG",
IUPAC.unambiguous_rna)
from Bio.Seq import Seq
from Bio.Seq import transcribe
from Bio.Data import CodonTable
table = CodonTable.unambiguous_dna_by_name["Standard"]
print(table)
DNA_Data = Seq("GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAG")
transcripted_DNA = transcribe(DNA_Data)
print(transcripted_DNA)
translated_Data = transcripted_DNA.translate()
print(translated_Data)
#Data used to produce the complement.
print(IUPACData.ambiguous_dna_complement)
#GC content
from Bio.SeqUtils import GC
nucleotide = Seq('GACTGACTTCGA', IUPAC.unambiguous_dna)
print("Nucleotide: " + nucleotide)
print("GC content: " + str(GC(nucleotide)))
#transcription
from Bio.Seq import transcribe
dna_seq = Seq('ATGCCGATCGTAT', IUPAC.unambiguous_dna)
print("dna_seq : " + nucleotide)
print("transcibed: " + transcribe(dna_seq))
rna_seq = transcribe(dna_seq)
print("rna_seq : " + rna_seq)
rna_seq_back_transcribed = rna_seq.back_transcribe()
print("rna_seq.bt: " + rna_seq_back_transcribed)
dna_template = rna_seq_back_transcribed.reverse_complement()
print("DNA templa:" + dna_template)
seqt = Seq('GAGATC', IUPAC.unambiguous_dna)
print(transcribe(seqt))
rna_seq = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGA", IUPAC.unambiguous_rna)
print(rna_seq)
print(rna_seq.translate())
def transcribe(self):
seq = "".join(self.src_text.GetValue().split()) #remove whitespace
print seq
self.dest_text.Clear()
self.dest_text.SetValue(transcribe(seq))
def main():
st.title("Transcription and Translation")
menu = ["Menu", "Protein Synthesis", "Upload FASTA File"]
choice = st.sidebar.selectbox("Select Activity", menu)
if choice == "Menu":
st.write(
"Transcription and translation take the information"
" in DNA and use it to produce proteins."
" Translation is the process where the information carried in "
"mRNA molecules is used to create proteins. The specific "
"sequence of nucleotides in the mRNA molecule provide the code for"
"the production of a protein with a specific sequence of amino acids."
)
st.image("dnatr.gif", use_column_width=True)
st.subheader("Use the sidebar to select activity")
elif choice == "Protein Synthesis":
st.subheader("Convert DNA to mRNA or to Protein sequence")
dna_seq = st.text_input("Enter DNA sequence")
if dna_seq:
mRNA = transcribe(dna_seq)
st.write("Transcribed Sequence is: ", mRNA)
protein_seq = translate(dna_seq)
st.write("Translated Sequence is: ", protein_seq)
st.image("dna.jpg", use_column_width=True)
elif choice == "Upload FASTA File":
st.subheader("Protein sequence")
sequence_file = st.file_uploader("Upload FASTA file",
type=["fasta", "fa", "txt"])
if sequence_file:
dna = SeqIO.read(sequence_file, "fasta")
if st.checkbox("Details of sequence"):
st.write(dna)
if st.checkbox("Length of sequence"):
st.write("length of dna sequence: ", len(dna))
dna_seq = dna.seq
translated_dna = dna_seq.translate()
if st.checkbox(
"Translation: Each row representing an amino acid sequence"
):
# split amino acids before stop codon. stop codon terminates translation
AA = translated_dna.split('*')
protein_sequence = [str(i) for i in AA]
st.write(protein_sequence)
# change to 3 letter amino acids instead of 1 letter AA
if st.checkbox("View 3 letter Amino Acids"):
st.write(seq3(translated_dna))
# Amino acid count
AA_analysed = ProteinAnalysis(str(translated_dna))
AA_freq = AA_analysed.count_amino_acids()
if st.checkbox("Amino acid Count"):
st.write(AA_analysed.get_amino_acids_percent())
# Visualize the amino acid count
if st.checkbox("Visualize Amino Acid count"):
plt.bar(AA_freq.keys(),
AA_freq.values(),
color="salmon",
edgecolor="black")
st.pyplot()
print(format_fast_string)
# Zusammenfügen bzw. Konkatenieren von Sequenzen
# ACHTUNG BEIM ARBEITEN von unterschiedlichen Seqs Typ check
dna_seq = Seq("ACGTA")
protein_seq = Seq("EVRNAK")
print ("Sum: ", protein_seq + dna_seq)
print(dna_seq)
print(dna_seq.complement())
print(dna_seq.reverse_complement())
# Transcription and Tanslation
coding_dna = Seq("ATGGCCATTGTAATG")
template_dna = coding_dna.reverse_complement()
messenger_rna = transcribe(coding_dna)
print(messenger_rna)
print(back_transcribe(messenger_rna))
print(translate(messenger_rna))
myThirdSequence = Seq("GATCGATGGGGGCTATCC")
print(GC(myThirdSequence))
# MutableSeq objects
print(dna_seq)
#dna_seq[0]="T" --> Nicht veränderbar!
mutable_seq = dna_seq.tomutable()
mutable_seq[0] = "T"
print(mutable_seq)
def transcribe(self):
seq = "".join(self.src_text.GetValue().split()) # remove whitespace
print seq
self.dest_text.Clear()
self.dest_text.SetValue(transcribe(seq))
from sys import argv
from Bio.Seq import translate
from Bio.Seq import transcribe
with open(argv[1], 'r') as in_file:
in_data = in_file.read().splitlines()
in_file.closed
dna = in_data[0]
protein = in_data[1]
rna = transcribe(dna)
for i in range(1,15):
if not (i == 7 or i == 8):
if (protein == translate(rna,table=i, stop_symbol='', to_stop=False)):
print i
