Restriction site = GAATTC

I want to cut the sequence at GA/ATTC

I tried split method in python but It does not cut at GA/ATTC. Please help

  • 4
    $\begingroup$ Have you looked up the documentation on working with restriction enzymes in biopython? biopython.org/DIST/docs/cookbook/Restriction.html#1.3 $\endgroup$
    – Devon Ryan
    Nov 8 '20 at 12:06
  • $\begingroup$ Nice documentation It really helped me. Thanks. $\endgroup$
    – amardeep
    Nov 8 '20 at 13:44
  • 3
    $\begingroup$ If you're able to do this after actually reading the documentation then please post a working example as an answer for others. $\endgroup$
    – Devon Ryan
    Nov 8 '20 at 14:01
  • $\begingroup$ The obvious bare native Python 'AAAAAAAAAAATTTTTTTTTTTGAATTCCCCCCCCCCCGGGGGGGGGGG'.split('GAATTC') produces what I expect. $\endgroup$
    – tripleee
    Nov 10 '20 at 6:03
  • 1
    $\begingroup$ @tripleee, your solution would not reflect the "true biology" The restriction enzyme cuts within the recognized bases and the two resulting fragments would contain a part (different parts obviously) of the restriction site. $\endgroup$
    – haci
    Nov 10 '20 at 14:45
import Bio
from Bio.Seq import Seq
my_seq = Seq("aaaaaaaaaaatttttttttttgaattccccccccccggggggggggg")
from Bio.Restriction import *

Actully the EcoRI cuts the DNA after G in restriction site GAATTC.

  • $\begingroup$ Okay my apologies, optical analysis is one of the reasons why bioinformatics is so important. You can mark your post as 'accepted'. $\endgroup$
    – M__
    Nov 10 '20 at 12:22

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