Marthey, S. | Search bioRxiv

bioRxiv2025

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

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

bioinformatics↗

bioRxiv2018

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig.

BackgroundFunctional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project (http://www.fragencode.org) aimed to profile the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells).\n\nResultsRNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically Associating Domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species.\n\nConclusionsWe report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.

genomics↗