In silico Double Digestion Fingerprinting (DDF)

Simulation of AFLP-PCR experiment

A classical AFLP-PCR experiment will be simulated:
  • Both endonucleases will be palindromic
  • Recognition sequence has no degenerated nucleotides
  • One endonuclease cleaves the genome very frequently and the other one fewer times.
  • According to Vos et al., only two fragments types will be amplified: RE1-RE2 and RE2-RE1. The other two fragment types are not amplified (RE1-RE1 and RE2-RE2 fragment types will form hairpins and other inhibitory processes)
When filling the form (see image below)...
  • we will check the checkbox for "AFLP", and the correct fragment types will be automatically selected,
  • in this example we will select restriction enzymes EcoRI and MseI from the lists of commercially available palindromic restriction enzymes,
  • although in the example the checkbox "For non-palindromic endonuclease discern complementary" is checked, unchecking it makes no difference in this case (due to palindromic nature of the selected endonucleases),
  • selective nucleotides are introduced in the form ("AC" for EcoRI site and "C" for MseI site)

Image for example 1

After clicking the "Amplify" buttom we will get 21 bands (see result here).

In the example below the same experiment is performed, but in this case the recognition sequence is introduced in the form.


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