{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Chan A"],"funding":["AI Health Innovation Cluster","Klaus Tschira Stiftung gGmbH","German Science foundation"],"pagination":["btaf536"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12552086"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["41(10)"],"pubmed_abstract":["<h4>Summary</h4>The development of third-generation sequencing technologies enables the detection of RNA modifications at single-molecule resolution. Specifically for direct RNA sequencing on the ONT platform, we have previously developed an m6A detection algorithm called mAFiA. Here, we present the updated method, now covering all 18 DRACH m6A contexts as well as the identification of pseudouridine sites (Ψ). Our modification level predictions compare favorably with orthogonal methods and respond to knockdown or knock out of writer proteins. The simultaneous detection of multiple modifications on a single RNA molecule opens up the possibility to study cross-modification interactions.<h4>Availability and implementation</h4>Ψ-co-mAFiA is available at https://github.com/dieterich-lab/psi-co-"],"journal":["Bioinformatics (Oxford, England)"],"pubmed_title":["Ψ-co-mAFiA: concurrent detection of pseudouridine and m6A in single RNA molecules."],"pmcid":["PMC12552086"],"funding_grant_id":["DFG TRR319","00.013.2021","439669440"],"pubmed_authors":["Chan A","Dieterich C","Naarmann-de Vries IS"],"additional_accession":[]},"is_claimable":false,"name":"Ψ-co-mAFiA: concurrent detection of pseudouridine and m6A in single RNA molecules.","description":"<h4>Summary</h4>The development of third-generation sequencing technologies enables the detection of RNA modifications at single-molecule resolution. Specifically for direct RNA sequencing on the ONT platform, we have previously developed an m6A detection algorithm called mAFiA. Here, we present the updated method, now covering all 18 DRACH m6A contexts as well as the identification of pseudouridine sites (Ψ). Our modification level predictions compare favorably with orthogonal methods and respond to knockdown or knock out of writer proteins. The simultaneous detection of multiple modifications on a single RNA molecule opens up the possibility to study cross-modification interactions.<h4>Availability and implementation</h4>Ψ-co-mAFiA is available at https://github.com/dieterich-lab/psi-co-","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Oct","modification":"2026-05-13T14:46:26.106Z","creation":"2026-05-13T14:25:01.989Z"},"accession":"S-EPMC12552086","cross_references":{"pubmed":["41002271"],"doi":["10.1093/bioinformatics/btaf536"]}}