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bioRxiv · 10.1101/2025.06.19.660341

WHOOPER Web application for Hands-On identification of proteins co-Occurrence among Phyla, focused on user ERgonomics

Marthey, S.·Baffo, N.·Martin, V.·Lodhi, L. Z.·Lisa, M.-N.·Andre, G.
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Abstract

SummaryWHOOPER is an intuitive web application designed to facilitate the analysis of protein co-occurrence across taxa. By integrating HHblits and HMMER, it enables efficient detection of remote homologs across extensive proteomic datasets. Its results interface combines an original data representation with advanced dynamic filtering functionalities to enable real-time exploration and exploitation of alignment data. Addressing key limitations of existing tools, WHOOPER streamlines workflows for studying protein prevalence, co-occurrence, and phylogenetic patterns, supporting seamless export for downstream evolutionary and functional genomics research. Availability and implementationThe code for Whopper is available 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 Contactsylvain.marthey@inrae.fr

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Marthey, S., Baffo, N., Martin, V., Lodhi, L. Z., Lisa, M.-N., Andre, G.. 2025-06-24. WHOOPER Web application for Hands-On identification of proteins co-Occurrence among Phyla, focused on user ERgonomics. https://doi.org/10.1101/2025.06.19.660341

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