OMAMO: orthology-based alternative model organism selection

Abstract

Summary: The conservation of pathways and genes across species has allowed scientists to use non-human model organisms to gain a deeper understanding of human biology. However, the use of traditional model systems such as mice, rats and zebrafish is costly, time-consuming and increasingly raises ethical concerns, which highlights the need to search for less complex model organisms. Existing tools only focus on the few well-studied model systems, most of which are complex animals. To address these issues, we have developed Orthologous Matrix and Alternative Model Organism (OMAMO), a software and a web service that provides the user with the best non-complex organism for research into a biological process of interest based on orthologous relationships between human and the species. The outputs provided by OMAMO were supported by a systematic literature review.

Availability and implementation: https://omabrowser.org/omamo/, https://github.com/DessimozLab/omamo.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

The web service interface. (A) The main browser page of OMAMO. The user can search a GO term (‘DNA repair’) or a GO ID (0006281). (B) The output page gives a list of species ranked based on the score, but the user has the option to sort the output based on the total number of orthologs or the average GO-based functional similarity by clicking on the up-down sorting icon. The user can view orthologs by clicking on the ‘+’ button.