{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T17:41:10Z","timestamp":1757612470239,"version":"3.44.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T00:00:00Z","timestamp":1756944000000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Research Initiatives support from City University of Hong Kong","award":["9610497"],"award-info":[{"award-number":["9610497"]}]},{"name":"Hong Kong Health and Medical Research Fund","award":["08194126"],"award-info":[{"award-number":["08194126"]}]},{"name":"General Research Fund","award":["11105524"],"award-info":[{"award-number":["11105524"]}]},{"name":"Early Career Scheme","award":["CityU 21100521"],"award-info":[{"award-number":["CityU 21100521"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Spliced leader (SL) trans-splicing occurs in a wide range of eukaryotes and plays a critical role in processing mRNAs derived from operon structures. However, current research on this mechanism remains limited, partly due to the difficulty in accurately identifying genuine SL trans-splicing events. The advent of long-read RNA sequencing technologies, such as direct RNA sequencing by Oxford Nanopore Technologies, offers a more promising avenue for detecting these events with greater resolution. Here, we present SLRanger, an integrated tool to detect SL sequences and predict operon structures in eukaryotic transcriptomes. SLRanger improves upon the traditional Smith\u2013Waterman (SW) alignment framework by incorporating an optimized scoring scheme tailored to SL detection in native long RNA reads. We primarily validated our method using direct RNA sequencing data from Caenorhabditis elegans, a well-established model organism for studying trans-splicing. Through a dynamic cutoff strategy, SLRanger robustly identified high-confidence SL-carrying reads. Leveraging the SL information, SLRanger achieved over 80% accuracy in operon gene prediction, recovering more than 70% of known operon genes in C. elegans. SLRanger was also applied to detect SL from cDNA long RNA reads and another trans-spliced species. Our results demonstrate that SLRanger not only provides a reliable approach for characterizing SL trans-splicing events but also serves as an effective framework for operon discovery, enabling transcriptomic analysis for operons and facilitating downstream data-mining applications.<\/jats:p>","DOI":"10.1093\/bib\/bbaf437","type":"journal-article","created":{"date-parts":[[2025,8,15]],"date-time":"2025-08-15T11:54:06Z","timestamp":1755258846000},"source":"Crossref","is-referenced-by-count":0,"title":["SLRanger: an integrated approach for spliced leader detection and operon prediction using long RNA reads"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-4863-3504","authenticated-orcid":false,"given":"Yanwen","family":"Shao","sequence":"first","affiliation":[{"name":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8315-5152","authenticated-orcid":false,"given":"Zhihao","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","place":["China"]}]},{"given":"Jinpeng","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, College of Computing, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1563-1844","authenticated-orcid":false,"given":"Runsheng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","place":["China"]},{"name":"Tung Biomedical Sciences Centre, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","place":["China"]},{"name":"Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Matter Science Research Institute (Futian) Shenzhen , 3 Binglang Road, Fubao Street, Futian District, Shenzhen, Guangdong, 518045 ,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,9,4]]},"reference":[{"key":"2025090409323407800_ref1","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.molbiopara.2007.02.003","article-title":"In vivo translation and stability of trans-spliced mRNAs in nematode embryos","volume":"153","author":"Cheng","year":"2007","journal-title":"Mol Biochem Parasitol"},{"key":"2025090409323407800_ref2","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1016\/S0168-9525(01)02499-4","article-title":"Evolutionary origin of SL-addition trans-splicing: still an 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