Purpose

Check the GC-content of all the primers.



In [3]:

    
from tinydb import TinyDB, Query
from Bio.SeqUtils import GC



In [4]:

    
# Open the database
db = TinyDB('primers.db.json')



In [8]:

    
# Query for primer 30 and 27
primer_30 = db.get(eid=30)['sequence']
primer_27 = db.get(eid=27)['sequence']



In [9]:

    
#Verify the sequence:
primer_30









    Out[9]:





'CACTATAGGCTAGCCTCGAGAGCAAAAGCAGGTCAATTATATTCAGTATGGAAAGAATAA'



In [10]:

    
primer_27









    Out[10]:





'ACTCTAGAGGTACCACGCGTGTAGAAACAAGGTCGTTTTTAAACTATTCAGCATTAATTG'



In [11]:

    
#Check the GC content of primer 30
GC(primer_30)









    Out[11]:





38.333333333333336

Conclusion

Trim primers to increase GC content



In [12]:

    
new_primer_30 = primer_30[0:55]



In [13]:

    
new_primer_30









    Out[13]:





'CACTATAGGCTAGCCTCGAGAGCAAAAGCAGGTCAATTATATTCAGTATGGAAAG'



In [19]:

    
end_base = 0
reverse_primer_27 = primer_27[::-1]
for base in reverse_primer_27:
    if base == 'G' or base == 'C':
        new_primer_27 = reverse_primer_27[end_base:]
        print(new_primer_27[::-1])
        break
    else:
        end_base+=1









    



ACTCTAGAGGTACCACGCGTGTAGAAACAAGGTCGTTTTTAAACTATTCAGCATTAATTG



In [16]:

    
primer_30









    Out[16]:





'CACTATAGGCTAGCCTCGAGAGCAAAAGCAGGTCAATTATATTCAGTATGGAAAGAATAA'



In [17]:

    
primer_30[::-1]









    Out[17]:





'AATAAGAAAGGTATGACTTATATTAACTGGACGAAAACGAGAGCTCCGATCGGATATCAC'



In [20]:

    
primer_27









    Out[20]:





'ACTCTAGAGGTACCACGCGTGTAGAAACAAGGTCGTTTTTAAACTATTCAGCATTAATTG'



In [21]:

    
new_primer_27









    Out[21]:





'GTTAATTACGACTTATCAAATTTTTGCTGGAACAAAGATGTGCGCACCATGGAGATCTCA'



In [ ]: