{"doi":"10.1101/2023.08.19.553943","title":"sRNAfrag: A pipeline and suite of tools to analyze fragmentation in small RNA sequencing data","abstract":"Fragments derived from small RNAs such as small nucleolar RNAs hold biological relevance. However, they remain poorly understood, calling for more comprehensive methods for analysis. We developed sRNAfrag, a standardized workflow and set of scripts to quantify and analyze sRNA fragmentation of any biotype. In a benchmark, it is able to detect loci of mature microRNAs fragmented from precursors and, utilizing multi-mapping events, the conserved 5' seed sequence of miRNAs which we believe may extraoplate to other small RNA fragments. The tool detected 1411 snoRNA fragment conservation events between 2/4 eukaryotic species, providing the opportunity to explore motifs and fragmentation patterns not only within species, but between. Availability: https://github.com/kenminsoo/sRNAfrag.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":410604,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9082,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":320405,"name":"Mayumi Jijiwa","orcid":"0000-0003-1596-856X","position":1,"is_corresponding":false},{"id":323027,"name":"Vedbar S. Khadka","orcid":"0000-0002-8652-2904","position":2,"is_corresponding":false},{"id":321924,"name":"Masaki Nasu","orcid":null,"position":3,"is_corresponding":false},{"id":1190903,"name":"Matthew Huo","orcid":null,"position":4,"is_corresponding":false},{"id":320407,"name":"Youping Deng","orcid":"0000-0002-5951-8213","position":5,"is_corresponding":false},{"id":1142226,"name":"K. Nakatsu","orcid":"0000-0002-7956-2270","position":0,"is_corresponding":true}],"reference_count":62,"raw_metadata":null,"created_at":"2026-07-19T01:21:35.071397Z","pmid":"37662282","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}