# WHOOPER : Web application for Hands-On identification of protein co-Occurrence among Phyla, focused on user ERgonomics.

Sylvain MARTHEY¹, Natacha BAFFO², María-Natalia LISA²,³ and Gwenaëlle ANDRÉ¹

1 Université Paris-Saclay, INRAE, MalAGE, Jouy-en-Josas, France

2 Instituto de Biología Molecular y Celular de Rosario (IBR CONICET-UNR), Ocampo y Esmeralda, Rosario S2002LRK, Argentina

3 Plataforma de Biología Estructural y Metabolómica (PLABEM), Ocampo y Esmeralda, Rosario S2002LRK, Argentina.

Corresponding Author: sylvain.marthey@inrae.fr

**Tool reference: https://whooper.migale.inrae.fr/**

**Keywords**

web application, remote homologs identification, evolution, user ergonomics, data visualization.

**Abstract**

Thinking the evolution of biological functions across different taxa requires studying the distribution and the prevalence of the functional units involved such as pathways, proteins, domains or folds, their co-occurrence within genomes and their co-evolution. While many tools exist to search for distant protein homologs: BLAST[1], HHblits [2], HMMER[3], Foldseek[4], the web servers handling these tools [5][6][7][4] neither allow the joint analysis of several proteins at the same time, nor an in-depth exploration through dynamic filtering, therefore they are not suitable for an easy, fast and accurate identification of co-occurrences of protein's homologs in genomes. Thus, we created the WHOPPER web application which combines the remote homologs detection power of HHsearch[8] with an interactive, ergonomic and innovative results exploitation environment, and follows the UX design principles of the Visual Information-Seeking Mantra: "Overview first, zoom and filter, then details-on-demand". [9]. Aligned with that vision, WHOPPER allows the user to: (i) align proteins of interest against hundreds of proteomes (ii) jointly visualize the massive results of alignments of these proteins against all proteomes through an innovative graphical view presenting the hits in their phylogenetic context (iii) use dynamic filtering of the results and navigation functionalities using contextual information and metadata of the hits (phylogeny, % identity, size, genomic localization, annotation, etc...) (iv) select and export results of interest in various formats to facilitate post-analysis. The application's code is accessible at: https://github.com/SmartBioInf/whooper. A public instance allowing the screening of more than 7500 reference proteomes from eukaryotes, bacteria, and archaea is available at: https://whooper.migale.inrae.fr/
References

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