Team:ETH Zurich/Modeling/Genome Static Analysis/RestrictionTable



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Result table on chromosomal digestion simulations
The table below summarizes the data obtained after simulating the digestion of E.Coli K12 MG1655 genome using the complete set of 713 restriction enzymes available at the REBASE database website. For each restriction enzyme, we computed which fragments of genome are obtained after digestion. Using the available annotation of Ecoli K12 MG1655 genome (that is, position of the genes on the chromosome), we calculated for each fragement the number of genes that are disrupted if it was to be removed from the genome. Then, we calculated statistical measures regarding the restriction enzyme effects, such as average size of the the fragments and their variance in size, and the average number of (all and only essential) genes and their variance in gene number.

Note 1: several restriction enzymes recognize the same base pattern, thus they have been summarized on the same line of the below table. These groups are 262. Note 2: the recognition sites displayed in the second field of the table, are expressed according to the MATLAB regular expression rules for nucleotides. Apart from the obvious meaning of a,t,c,g there are special characters such as R for Purine([AG]), Y for Pyrimidine ([TC]), K for Keto ([GT]), M for Amino [AC]). For the full detail look at the MATLAB help page.