How can I simulate enzyme digestion of a eukaryotic genome?

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Margot Paris

Hi Tauras,

you can try ISIF: http://www-leca.ujf-grenoble.fr/moyens-techniques/logiciels/article/population-genomics-software.

I am not up to date, and you can probably find more recent programs. But ISIF can digest genomes in silico without size limitation. The description of the program can be find here: https://www.researchgate.net/publication/225186276_In_silico_fingerprinting_(ISIF)_a_user-friendly_in_silico_AFLP_program

All the best for your analyses

Article In silico fingerprinting (ISIF): A user-friendly in silico A...

Juan Luis Mateo

I use the restrict command from the EMBOSS suite (http://emboss.sourceforge.net/apps/cvs/emboss/apps/restrict.html). There is also an online version of it (http://emboss.bioinformatics.nl/cgi-bin/emboss/restrict) but for genome wide restriction the command line version will be better. For vertebrate genomes it will take only a few minutes.

Best,

Juan