biostudies-literatureCullen JNNational Center for Advancing Translational SciencesNCATS NIH HHSUC Davis Center for Equine HealthGrayson-Jockey Club Research FoundationCollege of Veterinary Medicine, University of MinnesotaNational Institute of Food and Agriculturee1011835https://www.ebi.ac.uk/biostudies/studies/S-EPMC12449019biostudies-literatureUnknown21(9)MicroRNAs (miRNAs) are essential regulators of gene expression, yet few comprehensive databases exist for miRNA expression in non-model species, limiting our ability to characterize their roles in gene regulation, development, and disease. Similarly, isomiRs - length and sequence isoforms of canonical miRNAs with potentially altered regulatory targets and functions - have received even less attention in non-model species, including the horse, leaving a critical gap in our understanding of their biological significance. To address these challenges, we developed an open-source, containerized pipeline for identifying and quantifying miRNAs and isomiRs (FARmiR: Framework for Analysis and Refinement of miRNAs), and an associated interactive browser (AIMEE: Animal IsomiR and MiRNA Expression ExpPLoS geneticsCharting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression.PMC12449019UL1 TR002494KL2 TR0024922020-67034-31739K12TR002492016-10133NRSP-8 Species Coordinator Funds2019-67015-293402024-67012-41761UL1TR002494Multistate Competitive Funds 2017-2020, 2020-2022Hill EWLindgren GCullen JNMetzger JDistl OWade CMMcCue MEVelie BDKlaerke DADurward-Akhurst SAMacHugh DEWaud BColeman SJValderrama Figueroa LSMickelson JRCalloe KGiulotto EOrlando LMackowski MBellone RRRaudsepp TStrand EFinno CJCapomaccio SCappelli KHamilton NAKatz LMMacLeod JNKalbfleisch TSCieslak JTozaki TTrachsel DSSilvestrelli MPetersen JLMurphy BAfalseCharting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression.MicroRNAs (miRNAs) are essential regulators of gene expression, yet few comprehensive databases exist for miRNA expression in non-model species, limiting our ability to characterize their roles in gene regulation, development, and disease. Similarly, isomiRs - length and sequence isoforms of canonical miRNAs with potentially altered regulatory targets and functions - have received even less attention in non-model species, including the horse, leaving a critical gap in our understanding of their biological significance. To address these challenges, we developed an open-source, containerized pipeline for identifying and quantifying miRNAs and isomiRs (FARmiR: Framework for Analysis and Refinement of miRNAs), and an associated interactive browser (AIMEE: Animal IsomiR and MiRNA Expression Exp2025-01-01T00:00:00Z2025 Sep2026-06-03T15:29:42.617Z2026-04-29T03:12:39.467ZS-EPMC124490194091164110.1371/journal.pgen.1011835