DirectASRM: Uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing

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ID: 318202
2026
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Abstract
Abstract Summary We developed DirectASRM, a comprehensive database for the systematic identification, integration, and annotation of allele-specific RNA modifications (ASRMs) from direct RNA sequencing data. DirectASRM enables single-base, transcript-level detection of ASRMs across multiple RNA modification types, diverse organisms and condition-specific contexts. The database further evaluates the confidence of each ASRM–SNP pair association within isoform context by jointly considering statistical evidence of allelic modification imbalance and independent support from external next-generation sequencing (NGS) – based RNA modification resources. DirectASRM also provides extensive functional annotations for ASRMs and their associated variants, including intra-sample transcript-level allele-specific expression (ASE) and allele-specific splicing, as well as additional post-transcriptional regulatory features such as miRNA binding, circRNA, RNA–protein interactions, and disease relevance. Overall, DirectASRM serves as a comprehensive resource that supports systematic investigation of the potential functional impact of genetic variants in epitranscriptomic regulation. Availability and implementation DirectASRM database is freely accessible at http://modinfor.com/DirectASRM/. DirectASRM pipeline is available at GitHub (https://github.com/jiayin1101/DirectASRM_pipeline) and Zenodo (DOI: https://doi.org/10.5281/zenodo.19876077). Supplementary information Supplementary data are available at Bioinformatics online.
Reference Key
openalex_W7165567205 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Jiayin Dai, Yu Zhang, Jiayi Li, Jiongming Ma, Kunqi Chen, Jia Meng, Daniel J. Rigden, Zhen Wei, Shaofeng Lin, Qingru Xu
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag432
URL
https://doi.org/10.1093/bioinformatics/btag432
Keywords Keywords not found

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