Simple example of assembly with pydna

In [1]:

    

from pydna.all import *


    

In [2]:

    

b  = Dseqrecord("agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
l  = Dseqrecord("AGGCATCTACTG")
c  = Dseqrecord("tctgatctactatctgactgtactgatctattgacactgtgatcattctagtgtattactc")
(b+l+c).looped().cseguid()


    

    
Out[2]:





3lbRRPpQjEh_wEXzw6DaCZx0VMQ

In [3]:

    

l


    

    
Out[3]:





Dseqrecord(-12)

In [4]:

    

frags = assembly_fragments( (primer_design(b), l, primer_design(c), primer_design(b)), 1)


    

In [5]:

    

b2 = pcr(frags[-1].forward_primer, frags[0].reverse_primer, b)


    

In [6]:

    

b2.figure()


    

    
Out[6]:





 5agctactgactattaggggt...atctactatctgactgtactgatcta3
                         |||||||||||||||||||||||||| tm 54.6 (dbd) 55.4
                        3tagatgatagactgacatgactagatTCCGTAG5
5cagctactgactattaggggt3
  |||||||||||||||||||| tm 54.6 (dbd) 55.3
 3tcgatgactgataatcccca...tagatgatagactgacatgactagat5

In [7]:

    

frags[1].figure()


    

    
Out[7]:





       5tctgatctactatctgactgtact...tgtgatcattctagtgtattactc3
                                   |||||||||||||||||||||||| tm 52.9 (dbd) 55.8
                                  3acactagtaagatcacataatgagt5
5TCTACTGtctgatctactatctgactgtact3
        |||||||||||||||||||||||| tm 54.6 (dbd) 54.8
       3agactagatgatagactgacatga...acactagtaagatcacataatgag5

In [8]:

    

from pydna.assembly import terminal_overlap


    

In [9]:

    

asm2 = Assembly( (b2, frags[1]), limit=1, algorithm = terminal_overlap)
asm2


    

    
Out[9]:





Assembly
fragments..: 69bp 69bp
limit(bp)..: 1
G.nodes....: 4
algorithm..: terminal_overlap

In [10]:

    

asm2.assemble_circular()[0].cseguid()


    

    
Out[10]:





3lbRRPpQjEh_wEXzw6DaCZx0VMQ

In [11]:

    

asm2.assemble_circular()[0].figure()


    

    
Out[11]:





 -|69bp_PCR_prod| 2
|                \/
|                /\
|                 2|69bp_PCR_prod| 2
|                                 \/
|                                 /\
|                                  2-
|                                    |
 ------------------------------------

In [12]:

    

frags = assembly_fragments( (b, l, primer_design(c)), 1)


    

In [13]:

    

frags


    

    
Out[13]:





[Dseqrecord(-61), Amplicon(74)]

In [14]:

    

frags[0].seq


    

    
Out[14]:





Dseq(-61)
agct..tcta
tcga..agat

In [15]:

    

frags[1].figure()


    

    
Out[15]:





             5tctgatctactatctgactgtact...tgtgatcattctagtgtattactc3
                                         |||||||||||||||||||||||| tm 52.9 (dbd) 55.8
                                        3acactagtaagatcacataatgag5
5aAGGCATCTACTGtctgatctactatctgactgtact3
              |||||||||||||||||||||||| tm 54.6 (dbd) 54.8
             3agactagatgatagactgacatga...acactagtaagatcacataatgag5