{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T18:24:02Z","timestamp":1774549442328,"version":"3.50.1"},"reference-count":25,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T00:00:00Z","timestamp":1774483200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Department of Pathology, University of Cambridge"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Small non-coding RNAs (sncRNA;\u2009&lt;\u2009200 nucleotide length) are of increasing research interest due to their key regulatory roles in a host of fundamental biological processes. For example, microRNAs (miRNAs), a specific class of sncRNAs, regulate gene expression through messenger RNA (mRNA) interactions, and their dysregulation is associated with disease. Classifying sncRNAs is an important bioinformatic task in small RNA-sequencing pipelines. Here we have developed an aligner called PymiRa, written in Python, to identify and quantify miRNAs from FASTA\/FASTQ sequencing files. Unlike other approaches, PymiRa utilises a Burrows-Wheeler algorithm to align an input file against a reference hairpin precursor FASTA file derived from miRBase, the online miRNA registry, permitting up to two mismatches at the 3\u2019 end of a read. Previous tools used either a Burrows-Wheeler genome alignment or dynamic programming alignment to precursors; we demonstrate that combining both approaches yields improved results and efficiency. Importantly, the PymiRa aligner accounts for 3\u2019 post-transcriptional modifications to miRNAs that typically occur. PymiRa is a fast, accurate, and publicly accessible aligner available via GitHub and\/or a webserver for sncRNA identification, including miRNAs, enabling accurate counts to be produced as part of a small RNA-sequencing pipeline. PymiRa will undergo relevant revisions over time e.g., with miRBase version updates. The PymiRa aligner will facilitate a deeper biological understanding of the landscape of sncRNA expression in normal physiological conditions and their dysregulation in disease states, including cancer.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1014114","type":"journal-article","created":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T17:39:37Z","timestamp":1774546777000},"page":"e1014114","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["PymiRa: A rapid and accurate classification tool for small non-coding RNAs, including microRNAs"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-8063-0167","authenticated-orcid":true,"given":"Zachary G. 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