OMAMO: orthology-based model organism selection

OMAMO is a tool that suggests the best model organism to study a biological process based on orthologous relationship between a species and human.

The user can consider several species as potential model organisms and the algorithm will rank them and report the output for a given biological process (searched as a GO term or a GO ID) is produced in the dataframe format.

Pipeline

Firstly, download the OMA dataset:

wget  https://omabrowser.org/All/OmaServer.h5  -O data/OmaServer.h5  #caution: 94GB

Secondly, using the file data/oma-species.txt find the five-letter UniProt code for species of interest. For example, consider three species Dicdyostelium discodeium , Neurospora crassa and Schizosaccharomyces pombe. Their UniProt codes are DICDI, NEUCR and SCHPO, respectively.

Then, run the code omamo_base.py for each species code (DICDI, NEUCR and SCHPO):

species="DICDI"
mkdir output; cd output

python3 ../omamo_base.py ../data/OmaServer.h5 ../data/go_positive_annotations.tsv ${species}

Once the code finished running, the outputs include ${species}2.csv files which should be combined to create a final dataframe using the code omamo_dataframe.py:

python3 omamo_dataframe.py output

where output is the name of the directory where the user wishes to save the output.

Finally, the output data frame is ready as a CSV file omamo_output_df.csv.

OMAMO Website

You can also visit the OMAMO website, where you can browse biological processes to study in 50 unicellular species.

Change log

Version 0.0.1

Initial release

Citation

Alina Nicheperovich, Adrian M Altenhoff, Christophe Dessimoz, Sina Majidian, “OMAMO: orthology-based model organism selection”, submitted to Bioinformatics journal.

License

OMAMO is a free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

OMAMO is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with OMAMO. If not, see http://www.gnu.org/licenses/.