pYPKa_Z_PDC1

Freezer ID

Strain#..: ?
Box......: ?
Position.: ?

Importing the pydna package. Pydna is open source, documentated here and has a support forum as well as a publication:

Pereira F, Azevedo F, Carvalho Â, Ribeiro GF, Budde MW, Johansson B: Pydna: a simulation and documentation tool for DNA assembly strategies using python. BMC Bioinformatics 2015, 16:142.



In [1]:

    
from pydna.all import *

Read the cloning vector from a local file file, description of pYPKa.



In [2]:

    
pYPKa =read("pYPKa.gb")

This vector should be a circular 3128 bp DNA molecule.



In [3]:

    
pYPKa









    Out[3]:




pYPKa.gb

The circular seguid checksum of pYPKa should be

aV1eIrzOiCjvw01yvKkxDXHKLMk



In [4]:

    
pYPKa.cseguid()









    Out[4]:





aV1eIrzOiCjvw01yvKkxDXHKLMk

Importing the restriction enzyme to be used for cloning from Biopython. ZraI



In [5]:

    
from Bio.Restriction import ZraI

This enzyme should cut only once in pYPKa.



In [6]:

    
pYPKa_ZraI = pYPKa.linearize(ZraI)

The template below comes from a Genbank record. Access to Genbank is needed in order to download the template. If you execute this script, change the email address below to your own. Always tell Genbank who you are, when using their web service.



In [7]:

    
gb =Genbank("bjornjobb@gmail.com")

The template is downloaded from Genbank below.



In [8]:

    
template = gb.nucleotide("BK006945.2 REGION: complement(234082..235036)")

The template is a 955 bp linear DNA fragment.



In [9]:

    
template









    Out[9]:




BK006945.2  234082-235036

The insert has the sequence shown below.



In [10]:

    
str(template.seq)









    Out[10]:





'AGGGTAGCCTCCCCATAACATAAACTCAATAAAATATATAGTCTTCAACTTGAAAAAGGAACAAGCTCATGCAAAGAGGTGGTACCCGCACGCCGAAATGCATGCAAGTAACCTATTCAAAGTAATATCTCATACATGTTTCATGAGGGTAACAACATGCGACTGGGTGAGCATATGTTCCGCTGATGTGATGTGCAAGATAAACAAGCAAGGCAGAAACTAACTTCTTCTTCATGTAATAAACACACCCCGCGTTTATTTACCTATCTCTAAACTTCAACACCTTATATCATAACTAATATTTCTTGAGATAAGCACACTGCACCCATACCTTCCTTAAAAACGTAGCTTCCAGTTTTTGGTGGTTCCGGCTTCCTTCCCGATTCCGCCCGCTAAACGCATATTTTTGTTGCCTGGTGGCATTTGCAAAATGCATAACCTATGCATTTAAAAGATTATGTATGCTCTTCTGACTTTTCGTGTGATGAGGCTCGTGGAAAAAATGAATAATTTATGAATTTGAGAACAATTTTGTGTTGTTACGGTATTTTACTATGGAATAATCAATCAATTGAGGATTTTATGCAAATATCGTTTGAATATTTTTCCGACCCTTTGAGTACTTTTCTTCATAATTGCATAATATTGTCCGCTGCCCCTTTTTCTGTTAGACGGTGTCTTGATCTACTTGCTATCGTTCAACACCACCTTATTTTCTAACTATTTTTTTTTTAGCTCATTTGAATCAGCTTATGGTGATGGCACATTTTTGCATAAACCTAGCTGTCCTCGTTGAACATAGGAAAAAAAAATATATAAACAAGGCTCTTTCACTCTCCTTGCAATCAGATTTGGGTTTGTTCCCTTTATTTTCATATTTCTTGTCATATTCCTTTCTCAATTATTATTTTCTACTCATAACCTCACGCAAAATAACACAGTCAAATCAATCAAA'

The seguid checksum of the template should be

hkhP46T3bzNGN9KmoUtxq3MJFy8



In [11]:

    
template.seguid()









    Out[11]:





hkhP46T3bzNGN9KmoUtxq3MJFy8

Two primers are used to amplify the insert:



In [12]:

    
f,r =parse(""">413_ScPDC1tpf
                      TTAAATAAGGGTAGCCTCCCCATA
                     >625_ScPDC1tpr_PacI
                      taattaaTTTGATTGATTTGACTGTGTTATTTTG""", ds=False)

insert =pcr(f, r, template)

The primers anneal on the template like this.



In [13]:

    
insert.figure()









    Out[13]:





       5AGGGTAGCCTCCCCATA...CAAAATAACACAGTCAAATCAATCAAA3
                            ||||||||||||||||||||||||||| tm 55.0 (dbd) 64.8
                           3GTTTTATTGTGTCAGTTTAGTTAGTTTaattaat5
5TTAAATAAGGGTAGCCTCCCCATA3
        ||||||||||||||||| tm 56.5 (dbd) 61.2
       3TCCCATCGGAGGGGTAT...GTTTTATTGTGTCAGTTTAGTTAGTTT5

A recombinant plasmid is formed by ligating the insert PCR product to the linear vector.



In [14]:

    
plasmid = (pYPKa_ZraI + insert).looped()

The plasmid sequence is rotated so that the origin is in the same position as for the cloning vector sequence.



In [15]:

    
pYPKa_Z_PDC1 = plasmid.synced(pYPKa)

Calculate cseguid checksum for the resulting plasmid. Should be

YvPl6_OYiWllqL32w33VzoDyBqE



In [16]:

    
pYPKa_Z_PDC1.cseguid()









    Out[16]:





YvPl6_OYiWllqL32w33VzoDyBqE

The file is named pYPKa_Z_PDC1tp



In [17]:

    
pYPKa_Z_PDC1.name = "pYPKa_Z_PDC1tp"
pYPKa_Z_PDC1.description = "pYPKa_Z_PDC1tp"

Stamp sequence with cSEGUID checksum



In [18]:

    
pYPKa_Z_PDC1.stamp()









    Out[18]:





cSEGUID_YvPl6_OYiWllqL32w33VzoDyBqE

Write sequence to a local file.



In [19]:

    
pYPKa_Z_PDC1.write("pYPKa_Z_PDC1.gb")









    




pYPKa_Z_PDC1.gb

Download pYPKa_Z_PDC1



In [20]:

    
from pydna.all import *
reloaded =read("pYPKa_Z_PDC1.gb")
assert reloaded.cseguid() in reloaded.definition



In [21]: