outline the routine for species represented in the QfO reference
proteome collection, as the sequences in these sets are available
pre-annotated from the HaMStR project page. Per default, this
information is stored in pathToHaMStR/weight_dir where
each species has its own directory.
- Create a directory to store the output of the annotation proce-
dure. Give this directory a meaningful name like pathTo-
HaMStR/data/AMPK_annoDir. - For every seed–ortholog pair, extract the precomputed feature
annotations. Run the scriptpathToHaMStR/bin/fas/annota-
tion.plscript for this purpose. Create a new directorypathTo-
HaMStR/data/AMPK_annoDir/singleProteins. - Extract now the feature architecture information for PRKAA1
from human. Note that the species names used here might
deviate from the ones in the actual distribution: pathTo-
HaMStR/bin/fas/annotation.pl -path¼pathToHaMStR/
weight_dir/HUMAN@9606 -name¼Q13131 -extract¼pathTo-
HaMStR/data/AMPK_annoDir/singleProteins/
homsa_PRKAA1. - Rerun the above command for the yeast ortholog of PRKAA1.
To do so, simply replaceYEAST@559292forHUMAN@9606,
set –name to P06782, and modify the “extract” path
accordingly. - Use the feature architectures extracted in the previous steps as
input for the script greedyFAS.py to calculate the FAS score
between the two proteins.pathToHaMStR/bin/fas/greedyFAS.
py -s pathToHaMStR/data/AMPK_annoDir/singleProteins/
homsa_PRKAA1 -p pathToHaMStR/data/AMPK_annoDir/
singleProteins/saccePRKAA1 -o 1 –r pathToHaMStR/weight-
dir/HUMAN@9606 -j prkaa1_homsa_sacce_FAS_Result.xml.
The parameters–rand–jspecify the species used for feature
weighting and the output file name, respectively. - To extract the corresponding feature architectures for a later
visualization, run the script pathToHaMStR/bin/visuals/par-
seArchitecture.pl: pathToHaMStR/bin/visuals/parseArchitec-
ture.pl -i prkaa1_homsa_sacce_FAS_Result.xml -g PRKAA.
Upon completion, the script will create an output file named
prkaa1_homsa_sacce_FAS_Result.xml.domains.
3.5 Visualizing
FAS-Enhanced
Phylogenetic Profile
Visualize and explore the FAS-enhanced phylogenetic profile with
the PhyloProfile application. This will result in a comprehensive
overview of the phyletic distribution of the pathway components.
- Install the PhyloProfile application. A simple way to do it is
using the git tools [37]:git clonehttps://github.com/BIONF/
PhyloProfile. You will need an up-to-date R installation to run
the PhyloProfile application.
Tracing AMPK Evolution 127