Below we load the file genes.rda containing a named vector genes. This vector contains the function descriptions of a set of genes. The names of this vector give the COG codes of these genes:

 

> head(genes, n = 10)
                                                               RCOG3478 
"Predicted nucleic-acid-binding protein containing a Zn-ribbon domain " 
                                                               CCOG1031 
                                 "Uncharacterized Fe-S oxidoreductase " 
                                                               SCOG3771 
                                          "Predicted membrane protein " 
                                                               KCOG1191 
               "DNA-directed RNA polymerase specialized sigma subunit " 
                                                               SCOG5230 
                                   "Uncharacterized conserved protein " 
                                                               JCOG0532 
                      "Translation initiation factor 2 (IF-2; GTPase) " 
                                                               CCOG1905 
                        "NADH:ubiquinone oxidoreductase 24 kD subunit " 
                                                               FCOG0461 
                                   "Orotate phosphoribosyltransferase " 
                                                               SCOG2904 
                       "Uncharacterized protein conserved in bacteria " 
                                                               ECOG0509 
                 "Glycine cleavage system H protein (lipoate-binding) " 
...

 

Question: Find all COG codes for functions containing an enzyme name. An enzyme can be recognised by their name ending on “ase” or “ases”. For this, you need to:

 

• Extract the COG code from the names. This consists of the numbers following the letters COG in the name. Store the result in a vector COG.
• Find at which positions in the vector genes an enzyme is described. Store the result in a vector isEnzyme.
• Use the information from the previous two steps to find only the COG codes of the enzymes. Store these in a vector called enzymCOG.