Genome Restriction Digestion - (Jul/18/2008 )
I want to digest genomic DNA from a bacteria. I have the complete sequence of the genome. Is there a program that allows you to load the genomic sequence, apply one or more restriction enzyme and predict expected fragment sizes between a certain range (ie. between 50 to 5000bp)?
VectorNTI does this sort of prediction with plasmid vectors, but I am unsure if it is possible with whole genomes?
There's a programme called Artemis that deals with the annotation of entire bacterial genomes. I am not very familiar with it but I know that Sanger use it and so there may be functions on it that allow for digestion predictions. Sorry I realise this is very vague.
If you just need an estimate, this can be easily obtained statistically. Determine the GC content of the organism's DNA, call it p. Take the recognition site, and for each G or C, multiply by p/2. For each A or T, multiply by (1-p)/2. Take the reciprocal of this number as the estimated base pair distance between cut sites.
This works well except in a few cases, such as the unexpectedly rare CTAG tetramer in E. coli, and the general excess rarity of CG dicodons.