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 BackTransPageView(request):
if request.method == "POST":
xseq = request.POST.get('sequence')
my_rna = validaterna(xseq)
if my_rna == "error":
messages.info(request, 'Invalid RNA sequence')
return render(request, "backtranscription.html")
else:
transseq = back_transcribe(my_rna)
return render(request, "backtranscription.html",{
'seq':my_rna ,
'transseq':transseq ,
})
else:
return render(request,"backtranscription.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
def back_transcribe(self):
seq = "".join(self.src_text.GetValue().split()) # remove whitespace
print seq
self.dest_text.Clear()
self.dest_text.SetValue(back_transcribe(seq))
def back_transcribe(self):
seq = "".join(self.src_text.GetValue().split()) #remove whitespace
print seq
self.dest_text.Clear()
self.dest_text.SetValue(back_transcribe(seq))
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)
#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)
translate(messenger_rna)
# Direct translation (DNA -> Protein
from Bio.Seq import Seq, translate
from Bio.Alphabet import IUPAC
coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG", IUPAC.unambiguous_dna)
translate(coding_dna)
# Set any relevant command line arguments
seqs_in = args.file_name
max_CDS_overlap = args.CDS_overlap
maximum_fold_energy = args.stem_dG
# Spawn RNAfold
rnafold = subprocess.Popen(["RNAfold", "-noPS"], bufsize=10000, stdin=subprocess.PIPE, stdout=subprocess.PIPE)
# Read in and process seqs
seqs_input = open(seqs_in,"r")
for seq in SeqIO.parse(seqs_input, "genbank"):
# Create a dictionary of the sequence and the reverse complement
ss = {}
ss['+'] = str(back_transcribe(str(seq.seq)))
# Uncomment to search both strands
#ss['-'] = str(reverse_complement(ss['+']))
# Extract CDS regions from annotations
ss_cds = [0 for x in range(len(ss['+']))]
for f in seq.features :
if f.type == 'CDS':
if f.sub_features != []:
# Subfeatures of the CDS -> Splicing
for g in f.sub_features:
for x in range(g.location.start.position,g.location.end.position):
ss_cds[x] = 1
else:
# No subfeatures of the CDS -> Unspliced in the coding region
# 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)
translate(messenger_rna)
# Direct translation (DNA -> Protein
from Bio.Seq import Seq, translate
from Bio.Alphabet import IUPAC
coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG",
IUPAC.unambiguous_dna)
translate(coding_dna)
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))
# 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)
mutableSeq = MutableSeq("GCCCATC")
mutableSeq[1] = "A"
print(mutableSeq)
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')
seqRec = SeqRecord(seq)
