pYPK1

pYPK1 is a version of pYPK0 that has a CEN6/ARS yeast origin of replication instead of the 2µ origin of replication present in pYPK0.

The URA3 marker is substituted for a bleomycin marker.



In [1]:

    
from pydna.all import *



In [2]:

    
pMEC1042 =read("pMEC1042.gb")



In [3]:

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



In [4]:

    
pCAPs = gb.nucleotide("AJ001614.1")



In [5]:

    
from Bio.Restriction import PvuI, BamHI, EcoRI

pCAPs_pvu   = pCAPs.linearize(PvuI)
stuffer, pMEC1042_EB = pMEC1042.cut(BamHI, EcoRI)
pMEC1042_EB, stuffer









    Out[5]:





(Dseqrecord(-3270), Dseqrecord(-14))



In [6]:

    
asm=Assembly([pMEC1042_EB, pCAPs_pvu], limit=245)



In [7]:

    
asm









    Out[7]:





Assembly
fragments..: 3270bp 3130bp
limit(bp)..: 245
G.nodes....: 4
algorithm..: common_sub_strings



In [8]:

    
candidate = asm.assemble_circular()[0]
candidate









    Out[8]:




 -|name|700
|       \/
|       /\
|       700|AJ001614_lin_rc|245
|                           \/
|                           /\
|                           245-
|                              |
 ------------------------------



In [9]:

    
pYPK1 = candidate.synced(pCAPs)



In [10]:

    
pYPK1.stamp()









    Out[10]:





cSEGUID_cBXvb5dxm6dsur7YGH-fQNjeUGg



In [11]:

    
pYPK1.locus = "pYPK1"



In [12]:

    
pYPK1.write("pYPK1.gb")









    




pYPK1.gb

DOWNLOAD



In [13]:

    
from pydna.all import *
reloaded=read("pYPK1.gb")
assert reloaded.cseguid() in reloaded.definition