AMPK Methods and Protocols

3. To later visualize the information for all pathway proteins in
   one go, you need to combine the contents of the files ending in
   “.domains” for all proteins and store it in a file namedAMPK.
   domains.


4. Combine the contents of all files ending in “.extended.profile”
   and store the information in the fileAMPK.extended.profile.


5. Recreate the “.matrix” file by running the commandpathTo-
   HaMStR/bin/visuals/parseOneSeq.pl –iAMPK.extended.profile
   –o AMPK.
   Feature Architecture Similarity (FAS) score calculation for pre-
   existing ortholog pairs.
   A post hoc FAS scoring of orthologs downloaded from
   public repositories is possible, yet it is a bit more complex. We

Fig. 6Feature architecture of the human PRKAA1 ortholog inD. melanogaster. The plot displays the results of
an InterProScan using theD. melanogasterprotein with the UniProt ID O18645 as query

126 Arpit Jain et al.