starter
This commit is contained in:
mpabi
commit
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#! /usr/bin/env python3
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# vim:fenc=utf-8
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#
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# Copyright © 2024 user <user@penguin>
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#
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# Distributed under terms of the MIT license.
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import os
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from Bio import Entrez, SeqIO
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from Bio.Seq import Seq
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from Bio.SeqFeature import SeqFeature, FeatureLocation
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from Bio.Restriction import RestrictionBatch, EcoRI, BamHI, HindIII
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from Bio.Graphics import GenomeDiagram
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from reportlab.lib import colors
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#%%
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# Ustawienia Entrez
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Entrez.email = "your_email@example.com" # Wpisz swój adres email
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# Funkcja do pobierania sekwencji z NCBI i zapisywania jej lokalnie
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def fetch_and_save_sequence(db, id, file_path):
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handle = Entrez.efetch(db=db, id=id, rettype="gb", retmode="text")
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record = SeqIO.read(handle, "genbank")
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handle.close()
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SeqIO.write(record, file_path, "genbank")
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return record
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# Funkcja do wczytywania sekwencji z lokalnego pliku
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def load_local_sequence(file_path):
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with open(file_path, 'r') as file:
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record = SeqIO.read(file, "genbank")
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return record
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# Ścieżki do lokalnych plików
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gfp_file_path = 'gfp_sequence.gb'
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plasmid_file_path = 'plasmid_sequence.gb'
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# ID dla sekwencji w NCBI
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gfp_id = "U87974"
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plasmid_id = "U96626"
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# Sprawdzanie i pobieranie sekwencji GFP
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if not os.path.exists(gfp_file_path):
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print(f"Plik {gfp_file_path} nie istnieje. Pobieranie z serwera NCBI...")
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gfp_record = fetch_and_save_sequence("nuccore", gfp_id, gfp_file_path)
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print(f"Pobrano i zapisano sekwencję GFP do pliku {gfp_file_path}.")
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else:
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print(f"Plik {gfp_file_path} istnieje. Wczytywanie danych z lokalnego pliku...")
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gfp_record = load_local_sequence(gfp_file_path)
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print(f"Wczytano dane z pliku {gfp_file_path}.")
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gfp_seq = str(gfp_record.seq)
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print(f"GFP Sequence: {gfp_seq[:60]}...")
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# Sprawdzanie i pobieranie sekwencji plazmidu
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if not os.path.exists(plasmid_file_path):
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print(f"Plik {plasmid_file_path} nie istnieje. Pobieranie z serwera NCBI...")
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record = fetch_and_save_sequence("nuccore", plasmid_id, plasmid_file_path)
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print(f"Pobrano i zapisano sekwencję plazmidu do pliku {plasmid_file_path}.")
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else:
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print(f"Plik {plasmid_file_path} istnieje. Wczytywanie danych z lokalnego pliku...")
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record = load_local_sequence(plasmid_file_path)
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print(f"Wczytano dane z pliku {plasmid_file_path}.")
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#%%
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# Dodanie sekwencji kodującej His6
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his6_tag = "CACCACCACCACCACCAC" # Sekwencja kodująca 6x histydynę (His6)
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# Sekwencja białka GFP z His6 tagiem na końcu
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gfp_seq_with_his6 = gfp_seq + his6_tag
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# Projektowanie starterów
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forward_primer = gfp_seq[:20] # Pierwsze 20 nukleotydów sekwencji GFP
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reverse_primer = str(Seq(gfp_seq_with_his6[-20:]).reverse_complement()) # Ostatnie 20 nukleotydów + His6
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print(f"Forward Primer: {forward_primer}")
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print(f"Reverse Primer: {reverse_primer}")
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# Miejsca cięcia restryktazy
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enzymes = RestrictionBatch([EcoRI, BamHI, HindIII])
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restriction_sites = enzymes.search(record.seq)
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# Utwórz diagram plazmidu
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diagram = GenomeDiagram.Diagram("pET-28a(+) Plasmid Map")
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track = diagram.new_track(1, name="Annotated Features", greytrack=True)
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feature_set = track.new_set()
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# Dodanie sekwencji kodującej GFP
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feature_set.add_feature(
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SeqFeature(FeatureLocation(0, len(gfp_seq)), strand=+1),
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name="GFP Coding Sequence",
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label=True,
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color=colors.lightblue
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)
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# Dodanie His6 tagu
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feature_set.add_feature(
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SeqFeature(FeatureLocation(len(gfp_seq), len(gfp_seq_with_his6)), strand=+1),
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name="His6 Tag",
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label=True,
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color=colors.lightgreen
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)
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# Dodanie forward primer
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feature_set.add_feature(
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SeqFeature(FeatureLocation(0, len(forward_primer)), strand=+1),
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name="Forward Primer",
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label=True,
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color=colors.orange
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)
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# Dodanie reverse primer
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feature_set.add_feature(
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SeqFeature(FeatureLocation(len(gfp_seq_with_his6) - len(reverse_primer), len(gfp_seq_with_his6)), strand=-1),
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name="Reverse Primer",
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label=True,
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color=colors.red
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)
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# Dodanie miejsc cięcia restryktazy
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for enzyme, sites in restriction_sites.items():
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for site in sites:
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feature_set.add_feature(
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SeqFeature(FeatureLocation(site, site + 1), strand=0),
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name=enzyme,
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label=True,
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color=colors.purple
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)
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# Rysowanie diagramu
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diagram.draw(format="circular", circular=True, pagesize='A4', start=0, end=len(record), circle_core=0.5)
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diagram.write("pdf/plasmid_map.pdf", "PDF")
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print("Zapisano diagram plazmidu do pliku 'plasmid_map.pdf'")
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@ -0,0 +1,66 @@
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LOCUS SCU87974 818 bp mRNA linear SYN 24-FEB-1997
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DEFINITION Synthetic construct modified green fluorescent protein GFP5-ER
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(mgfp5-ER) mRNA, complete cds.
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ACCESSION U87974
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VERSION U87974.1
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KEYWORDS .
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SOURCE synthetic construct
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ORGANISM synthetic construct
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other sequences; artificial sequences.
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REFERENCE 1 (bases 1 to 818)
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AUTHORS Siemering,K.R., Golbik,R., Sever,R. and Haseloff,J.
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TITLE Mutations that suppress the thermosensitivity of green fluorescent
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protein
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JOURNAL Curr. Biol. 6 (12), 1653-1663 (1996)
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PUBMED 8994830
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REFERENCE 2 (bases 1 to 818)
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AUTHORS Haseloff,J., Siemering,K.R., Prasher,D. and Hodge,S.
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TITLE Removal of a cryptic intron and subcellular localisation of green
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fluorescent protein are required to mark transgenic Arabidopsis
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plants brightly
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JOURNAL Proc. Natl. Acad. Sci. U.S.A. (1997) In press
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REFERENCE 3 (bases 1 to 818)
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AUTHORS Siemering,K.R., Golbik,R., Sever,R. and Haseloff,J.
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TITLE Direct Submission
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JOURNAL Submitted (31-JAN-1997) Division of Cell Biology, MRC Laboratory of
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Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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FEATURES Location/Qualifiers
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source 1..818
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/organism="synthetic construct"
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/mol_type="mRNA"
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/db_xref="taxon:32630"
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gene 1..818
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/gene="mgfp5-ER"
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CDS 21..812
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/gene="mgfp5-ER"
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/note="contains codon usage changes that disrupt a cryptic
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plant intron, mutations that increase the thermotolerance
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and change the spectral characteristics of the protein, and
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sequences that code for signal peptides that result in
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retention of the protein in the plant endoplasmic
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reticulum"
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/codon_start=1
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/transl_table=11
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/product="modified green fluorescent protein GFP5-ER"
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/protein_id="AAB47999.1"
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/translation="MKTNLFLFLIFSLLLSLSSAEFSKGEELFTGVVPILVELDGDVNG
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HKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDF
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FKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLE
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YNYNSHNVYIMADKQKNGIKANFKTRHNIEDGGVQLADHYQQNTPIGDGPVLLPDNHYL
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STQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKHDEL"
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ORIGIN
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1 ggatccaagg agatataaca atgaagacta atctttttct ctttctcatc ttttcacttc
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61 tcctatcatt atcctcggcc gaattcagta aaggagaaga acttttcact ggagttgtcc
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121 caattcttgt tgaattagat ggtgatgtta atgggcacaa attttctgtc agtggagagg
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181 gtgaaggtga tgcaacatac ggaaaactta cccttaaatt tatttgcact actggaaaac
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241 tacctgttcc atggccaaca cttgtcacta ctttctctta tggtgttcaa tgcttttcaa
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301 gatacccaga tcatatgaag cggcacgact tcttcaagag cgccatgcct gagggatacg
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361 tgcaggagag gaccatcttc ttcaaggacg acgggaacta caagacacgt gctgaagtca
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421 agtttgaggg agacaccctc gtcaacagga tcgagcttaa gggaatcgat ttcaaggagg
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481 acggaaacat cctcggccac aagttggaat acaactacaa ctcccacaac gtatacatca
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541 tggccgacaa gcaaaagaac ggcatcaaag ccaacttcaa gacccgccac aacatcgaag
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601 acggcggcgt gcaactcgct gatcattatc aacaaaatac tccaattggc gatggccctg
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661 tccttttacc agacaaccat tacctgtcca cacaatctgc cctttcgaaa gatcccaacg
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721 aaaagagaga ccacatggtc cttcttgagt ttgtaacagc tgctgggatt acacatggca
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781 tggatgaact atacaaacat gatgagcttt aagagctc
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//
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File diff suppressed because one or more lines are too long
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@ -0,0 +1,131 @@
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LOCUS MMU96626 4742 bp DNA linear ROD 07-FEB-1998
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DEFINITION Mus musculus chondroadherin gene, complete cds.
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ACCESSION U96626
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VERSION U96626.1
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KEYWORDS .
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SOURCE Mus musculus (house mouse)
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ORGANISM Mus musculus
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Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
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Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
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Muroidea; Muridae; Murinae; Mus; Mus.
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REFERENCE 1 (bases 1 to 4742)
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AUTHORS Landgren,C., Beier,D.R., Fassler,R., Heinegard,D. and Sommarin,Y.
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TITLE The mouse chondroadherin gene: characterization and chromosomal
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localization
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JOURNAL Genomics 47 (1), 84-91 (1998)
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PUBMED 9465299
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REFERENCE 2 (bases 1 to 4742)
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AUTHORS Landgren,C. and Sommarin,Y.
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TITLE Direct Submission
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JOURNAL Submitted (07-APR-1997) Connective Tissue, Cell and Molecular
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Biology, Lund 22100, Sweden
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FEATURES Location/Qualifiers
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source 1..4742
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/organism="Mus musculus"
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/mol_type="genomic DNA"
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/db_xref="taxon:10090"
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/chromosome="11"
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/map="between D11Mit36 and D11Mit10"
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mRNA join(671..1490,3420..3583,3831..3976,4202..4742)
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/product="chondroadherin"
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exon 671..1490
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/number=1
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CDS join(720..1490,3420..3583,3831..3972)
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/codon_start=1
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/product="chondroadherin"
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/protein_id="AAC39963.1"
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/translation="MARALLFSLVFLAILLPALAACPQNCHCHGDLQHVICDKVGLQKI
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PKVSETTKLLNLQRNNFPVLAANSFRTMPNLVSLHLQHCNIREVAAGAFRGLKQLIYLY
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LSHNDIRVLRAGAFDDLTELTYLYLDHNKVSELPRGLLSPLVNLFILQLNNNKIRELRA
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GAFQGAKDLRWLYLSENALSSLQPGSLDDVENLAKFHLDKNQLSSYPSAALSKLRVVEE
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LKLSHNPLKSIPDNAFQSFGRYLETLWLDNTNLEKFSDAAFSGVTTLKHVHLDNNRLNQ
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LPSSFPFDNLETLTLTNNPWKCTCQLRGLRRWLEAKASRPDATCSSPAKFKGQRIRDTD
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ALRSCKSPTKRSKKAGRH"
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exon 3420..3583
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/number=2
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exon 3831..3976
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/number=3
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exon 4202..4742
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/number=4
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ORIGIN
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1 gagctcttac gggcctggtg ccactgggct ccgagaaggg gcagagccaa acgcacggct
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61 gtcagctagc ctctgcaacc agctccccca cctccttggg ataaactgag gaacccagaa
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121 gcgggagccc aacccacagc agctctcacg ctccgcctgc gccgcacaac agtcccatta
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181 aagcgccgcc ggctggccga ccgcggtgag acgcatccgg ctgtcgggcc ccacttcctc
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241 cctcccggag tccagggtga cctgtctgcc aagggtgtat gggggaagga gacgtagaga
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||||||
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301 actcaaactt gagcaaataa ataagttctg ggaacacttc cctctgccca gtggaaattc
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361 agaagcccct cgacacacct atcaccgtcc accccacctc ggggtgttgg tccagataga
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421 ggagggtagg ggaaggtgca gcataatgtt tgcaaacagg aaccaagggg ttggggttca
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481 ggggaagggc cctcagccct acacacggtc tcctgctgtg aaaagaggcc cccagccatc
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541 gaggatgggg acgcatctct gggcgggaag gggttaaatc agtggcttcg gtgctccacg
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601 tagtagctgg ctccgctgcc aactgcggtc aaggctgccc tataaatggg ccgggagacc
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||||||
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661 cgagagtcga ggacttgtcg ctgccttagc ccccagccca ggctcaaggc gttctaacca
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721 tggcccgcgc gctcttattc agtctggtct ttcttgccat cctcctgcct gcgctagccg
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781 cctgccccca aaactgccac tgccatggag atctgcagca tgtcatctgc gacaaggtgg
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||||||
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841 ggctgcagaa gatccccaag gtatcagaga caaccaaact gctcaatctc cagcgcaaca
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901 acttcccggt gctggctgcc aactcgtttc ggaccatgcc gaacctggtc tccctgcacc
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||||||
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961 tgcaacactg caacatccgc gaggtggcgg ctggtgcctt ccgaggcctg aagcagctta
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||||||
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1021 tctacctgta cctgtcccac aacgacatcc gggtattgcg agctggagcc ttcgacgacc
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1081 tgactgaact cacttacctc tatctagacc acaacaaagt gtcggaactg ccccgggggt
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||||||
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1141 tgctctctcc tctggtcaac ctcttcatct tgcaactcaa caacaacaaa atccgagagc
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1201 tgcgtgctgg agctttccag ggggccaagg acctgcgctg gctctacctg tcagaaaatg
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1261 ccctcagttc cctgcagcct ggttccctgg atgatgtgga gaacctagcc aagttccacc
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1321 tggacaagaa ccagctgtct agctacccct cagccgccct gagcaaactt cgggtggtgg
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1381 aggagctgaa gctgtctcac aaccctctga agagcatccc agacaatgcc ttccagtcct
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1441 tcggtagata tctggagacc ctctggctgg ataacaccaa cctggagaag gtaagtgccc
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||||||
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1501 cagctgcagt tctcccggct ctttctagga tgccacccca ggaaccacat cgggacagca
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1561 ttccctcctc ctggactcct tgtcactcag attatcctcc aaagcaaggg gcctttgcca
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1621 cttctctctg cattgacaca cacccctccc catccttctc acccttacct ggtcccgagg
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1681 cttctcagac agggctctct tgggactcct tgtaagagat ggaactgttc tggtcccaca
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||||||
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1741 aatggcctct ggggaggcat ctgccccaga ccccacggtt aacagcagac acctcttcct
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1801 gttggacttt ccacccctct cttaccagtc tcctgcaagc ctaccatttc ataaaggaag
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1861 gtttgtctac tgaggcacct tccagaagct gagagaacac aaagagtgcc tgttcccagt
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||||||
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1921 gggtgctggc ctgtgttgct aaggtaaagt gagaggccag aggatgaatt ggggagcagg
|
||||||
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1981 taccttaagg agaactctcc cacaccctcg tcccattccc tccgtgggtc gaaacacact
|
||||||
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2041 caattttatt gcaacctcgg gtcgatttca aatatggacg ggaaaccaag acacggagac
|
||||||
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2101 ctgacttggc ttcaccgagt tgctggcttg gtgctcttgc agcccgtgaa taaacacatg
|
||||||
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2161 caatccctgg cacacgcccc cccaagtgtc tcctcagagc acagactgac tgtctcactg
|
||||||
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2221 tccagcagac agtttgttga cttttgcttt ccccagtcac cagatcccag actcctcaat
|
||||||
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2281 tcttcctccc ttgggatgct caggctagcc tggtcggggc tgtctaggag caaagtcctt
|
||||||
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2341 ttcagggaat caccctggta cacaacacag tttcagccag aaggttcggg cagagaccag
|
||||||
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2401 agcgaggtag agtagttttg tttgtagaga acgtcacagc ccaatctggt ctgtgagagg
|
||||||
|
2461 tcacagatac tgagctgagg acagaacgcc aaccttatct aggtagatgg agccttctgg
|
||||||
|
2521 gtggatcttc tttagcctgg cctcacccca gctaaatgta gaccacccta gtgacaaaac
|
||||||
|
2581 agtggccagt agaacagcat acgaaggctg atttagaatg aggaggccaa agccgggcgt
|
||||||
|
2641 ggtagcgcac gccttcaatc ccagtacctg ggaggcaaag gcaggcgaat ttctaagttc
|
||||||
|
2701 gaggccagcc tggtctacag agtgagttcc aggacagcca ggactacaca gagaaaccct
|
||||||
|
2761 gtctcacaaa aaccaaaaag aaaaaagaaa aaaaaaagaa tgaggaggcc agagagaact
|
||||||
|
2821 ggcaccaagg ctcagaggag ggcaccaata catttcctct ggagccatcc atcctggcca
|
||||||
|
2881 aagtgcccac agagagctcc acaaatagca tctagcagaa ggcagagcaa tgaggacacc
|
||||||
|
2941 actgggggaa atcctgggac cagggggctg tggggagcct gggctcactg cccatcccac
|
||||||
|
3001 caaaccctga ccaggttcac cgtgtgcccg ccccaggcac actgcccatc ccaccaaaca
|
||||||
|
3061 ctgaccaggt tcaccgtgtg cccgcccggg cactcaaagc caagctctgc ctgctcccca
|
||||||
|
3121 gacccagtgt ttgtgcaggg aggtgctgcc taggaggtgg gggacagggt gtggtcctgc
|
||||||
|
3181 agctactgtt tactagctag gtgaccctgt ccaaaggact gaaccttttc cgtttacaca
|
||||||
|
3241 ttgggaagga ccccttccct ctctctctct ctctcaaaaa aaggtgttgt ggaggatgac
|
||||||
|
3301 atcattgtgg ctcctcaaca ggccagggcg tgtgtccagg gaaaagacaa ccctggtcct
|
||||||
|
3361 ctgagaaggg agccaggaga ctgagttgag gtgctcactc tgcctccctc acctcacagt
|
||||||
|
3421 tctcagatgc tgccttctcg ggtgtgacca cactgaaaca cgtccatctg gacaacaacc
|
||||||
|
3481 gcctgaacca actgccttcc tccttcccct ttgacaacct ggagaccctc actctcacca
|
||||||
|
3541 acaacccatg gaaatgcacc tgccagctcc gtggccttcg gcggtgagaa tattcctcca
|
||||||
|
3601 tataaccccc agactgccgt ccacatgaca gacggtccta gagtaggaca gcctggacat
|
||||||
|
3661 cctagtcagc tacctagcat gtcgggtact gagtggttcc cttctctcat ttgtcaaatg
|
||||||
|
3721 aagatgacaa ctccagatat ttctatggcc atagtccatc ccggtcactg tccctttccc
|
||||||
|
3781 aagccttccc acccagcttt tccaagccca gcaactcttt gtctctgtag gtggttggaa
|
||||||
|
3841 gccaaggctt ctcgaccgga tgctacctgc tcctcgccag ccaagttcaa gggtcagcgg
|
||||||
|
3901 attcgtgaca cagatgccct tcgcagctgc aaatccccga ccaagaggtc caagaaagct
|
||||||
|
3961 ggccgccatt aaacaggtgg gggctgggta gggaggccac cacggtctac ctttggaaat
|
||||||
|
4021 tccagatggg gtgctgctat atcccatgac accacttccg gaggagcaat cagttccctg
|
||||||
|
4081 tcttacaaga aaaggaggga ggacaggata acctctccca tggcttggcc taggacgtcc
|
||||||
|
4141 atgggtccct ttaatgactc tgggtgactg gaatcctaat acccatcttc tctcactata
|
||||||
|
4201 ggtcctgatc cagccagtcc tggcgactgc cttccgctgg agagactact gacgttccct
|
||||||
|
4261 cccatcatcc acaccttctc ctacagcctc tgcggatgca cagcgctgcc ccgcccccgc
|
||||||
|
4321 ccccacctag gtacatcctg gcaggggcac tgggctctct atcaccatcc cagctccacc
|
||||||
|
4381 cagtggggtc ctaggaaaga cacagaatcc ctccccagcc actgtgtctg ggctctgcca
|
||||||
|
4441 tggctccttt gagagaagct attgtagaac ctcctaccct ctgtccatcg gagctaaagc
|
||||||
|
4501 gcagtggtca ttgggatgac cacgttatta ccaccttcct cggttccctc tgtccctgcc
|
||||||
|
4561 atttggaaac aaacatcagg cccctgaccc accctgattg ccagaaagaa tttcaggccc
|
||||||
|
4621 atgccccaac tctgccagtt cctgcctgcc aggacatgct accaggatac cagtagcgct
|
||||||
|
4681 tggctgcata tccttcctgt ttgcgctcca gatttctata aacataaatg tatgtgtgtt
|
||||||
|
4741 ca
|
||||||
|
//
|
||||||
Loading…
Reference in New Issue