<jupyter_start><jupyter_text>pLBL3_PiXI_optThe pLBL_PiXI is the [pLBL3 vector](pLBL3.ipynb) with the xylose isomerase gene from [Piromyces sp](https://en.wikipedia.org/wiki/Piromyces) located between the TEF1 promoter and the RPS7B terminator.The XI gene is the codon optimized gene described by [Brat et al. 2009](https://www.ncbi.nlm.nih.gov/pubmed/19218403).<jupyter_code>from pydna.all import *
pLBL3 = read("pLBL3.gb")
p426H7_opt_XI_Piro = read("../data/raw/fwdcodonoptimizedpiromycesxyloseisomerasegene/p426H7-opt.XI-Piro.gbk")
p426H7_opt_XI_Piro
p426H7_opt_XI_Piro.list_features()
PiXI_opt_orf = p426H7_opt_XI_Piro.extract_feature(0)
print(str(PiXI_opt_orf.translate().seq))
product = primer_design(PiXI_opt_orf)
from Bio.Restriction import AjiI
pLBL3_lin = pLBL3.linearize(AjiI)
slask, product_tails = circular_assembly_fragments((pLBL3_lin,Dseqrecord("AA"),product), overlap=35)
product_tails.figure()
product_tails.name = "PiXI_opt"
asm = Assembly((pLBL3_lin, product_tails))
asm
candidates = asm.assemble_circular()
candidates
candidate = candidates[0]
candidate
pLBL3_PiXI_opt = candidate.synced(pLBL3)
pLBL3_PiXI_opt
assert pLBL3_PiXI_opt.cseguid() =="DR2uis2xRt9A-Gc_zYizL1N_jiI"
pLBL3_PiXI_opt.stamp()
pLBL3_PiXI_opt.locus = "pLBL3_PiXI_opt"
pLBL3_PiXI_opt.write()<jupyter_output><empty_output><jupyter_text>The primers below are the ones actually used. These were manually designed but give the same result as the ones designed above.<jupyter_code>fp, rp = parse_primers("""
>1125_PiXYLAoptfw
gaggaacgccaggttgcccactttctcactagtgacctgcagccgacaaATGGCTAAGGAATACTTCC

>1124_PiXYLAoptrv
tggattaaaaatttaaatcctgatgcgtttgtctgcacagatggcacTTATTGGTACATAGCAACAATAG""")
product_tails2 = pcr(fp,rp,p426H7_opt_XI_Piro)
asm2 = Assembly((pLBL3_lin, product_tails2))
asm2
assert asm2.assemble_circular()[0].cseguid() == "DR2uis2xRt9A-Gc_zYizL1N_jiI" == pLBL3_PiXI_opt.cseguid()<jupyter_output><empty_output>
StarcoderdataJupyterStructuredCleanDedup