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8.2.3
Final preparation
To automatically download, format and test the ortholog database as well as to
perform some final tests, we call the perl script ”prepare analysis.pl” as follows:
perl perl_scripts/prepare_analysis.pl
8.3
Orthology Assignment
Now we want to assign orthology to our EST sequences in folder
root_path/est_libraries/
Using default settings in the configuration file, we start the analysis on our
single computer by typing:
perl perl_scripts/start_orthology_assignment_single.pl
After the analysis has finished, the project folder (”root path/TEST ANALYSIS/”)
will contain the following directories:
annotations basis_hits
The results have been saved to the folder
root_path/TEST_ANALYSIS/basis_hits/
and contain the following OGs:
KOG0003
KOG0019
KOG0020
KOG0027
KOG0179
KOG0213
The EST sequence as well as its translation will be saved in the corresponding
OG subfolder.
E.g. an EST sequence from Daphina pulex assigned to ’KOG0213’ will be saved
as
KOG0213_Daphnia_pulex_prot_hits.fasta
KOG0213_Daphnia_pulex_nucl_hits.fasta
in ”root path/TEST ANALYSIS/basis hits/KOG0213/”. Annotations are saved
in
root_path/TEST_ANALYSIS/annotations/
This folder will now contain the annotation for all our taxa in the study. The
folder comprises:
Aspergillus_niger.txt
Ciona_intestinalis.txt
Daphnia_pulex.txt
Lottia_gigantea.txt
Monosiga_brevicollis.txt
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