In silico Double Digestion Fingerprinting (DDF)

Simulation of AFLP-PCR experiment when using only one endonuclease

This approach has not yet been tried in the lab.

We will explain the theoretical experiment performed when filling the form as shown in the picture:


In this experiment we will use only one endonuclease (BsaJI with recognition sequence C'CNNG_G) to perform an AFLP-PCR-like experiment. The maximum length of fragments has been set up to 3000 bp.

Endonuclease BsaJI cuts E. coli K12 genome 11483 times (more info here), so 11483 fragments will be yielded.

By using the experimental conditions introduced in the form, in the first step, two kinds of fragments will be computed:




In a second step, as sequence CCNNGG has been introduced in the form as "Exclusion sequence", all fragments including within their sequence the "Exclusion sequence" will be removed from final results.   

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