{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T07:19:31Z","timestamp":1775027971353,"version":"3.50.1"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,12]],"date-time":"2019-01-12T00:00:00Z","timestamp":1547251200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Strategic Priority Research Programme of the Chinese Academy of Sciences","award":["XDB13040500"],"award-info":[{"award-number":["XDB13040500"]}]},{"name":"Strategic Priority Research Programme of the Chinese Academy of Sciences","award":["XDA08020102"],"award-info":[{"award-number":["XDA08020102"]}]},{"name":"National Key Research and Development Programme of China","award":["2017YFC0907502"],"award-info":[{"award-number":["2017YFC0907502"]}]},{"name":"National Key Research and Development Programme of China","award":["2015AA020108"],"award-info":[{"award-number":["2015AA020108"]}]},{"name":"National Key Research and Development Programme of China","award":["2016YFE0206600"],"award-info":[{"award-number":["2016YFE0206600"]}]},{"name":"International Partnership Programme of the Chinese Academy of Sciences","award":["153F11KYSB20160008"],"award-info":[{"award-number":["153F11KYSB20160008"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31200978"],"award-info":[{"award-number":["31200978"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Open Biodiversity and Health Big Data Initiative of IUBS"},{"name":"The 13th Five-year Informatization Plan of Chinese Academy of Sciences","award":["XXH13505-05"],"award-info":[{"award-number":["XXH13505-05"]}]},{"DOI":"10.13039\/501100004052","name":"The King Abdullah University of Science and Technology","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004052","name":"KAUST","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Base Research Funds","award":["BAS\/1\/1606-01-01"],"award-info":[{"award-number":["BAS\/1\/1606-01-01"]}]},{"name":"Strategic Priority Research Programme of the Chinese Academy of Sciences"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The significance of long non-coding RNAs (lncRNAs) in many biological processes and diseases has gained intense interests over the past several years. However, computational identification of lncRNAs in a wide range of species remains challenging; it requires prior knowledge of well-established sequences and annotations or species-specific training data, but the reality is that only a limited number of species have high-quality sequences and annotations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here we first characterize lncRNAs in contrast to protein-coding RNAs based on feature relationship and find that the feature relationship between open reading frame length and guanine-cytosine (GC) content presents universally substantial divergence in lncRNAs and protein-coding RNAs, as observed in a broad variety of species. Based on the feature relationship, accordingly, we further present LGC, a novel algorithm for identifying lncRNAs that is able to accurately distinguish lncRNAs from protein-coding RNAs in a cross-species manner without any prior knowledge. As validated on large-scale empirical datasets, comparative results show that LGC outperforms existing algorithms by achieving higher accuracy, well-balanced sensitivity and specificity, and is robustly effective (&amp;gt;90% accuracy) in discriminating lncRNAs from protein-coding RNAs across diverse species that range from plants to mammals. To our knowledge, this study, for the first time, differentially characterizes lncRNAs and protein-coding RNAs based on feature relationship, which is further applied in computational identification of lncRNAs. Taken together, our study represents a significant advance in characterization and identification of lncRNAs and LGC thus bears broad potential utility for computational analysis of lncRNAs in a wide range of species.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>LGC web server is publicly available at http:\/\/bigd.big.ac.cn\/lgc\/calculator. The scripts and data can be downloaded at http:\/\/bigd.big.ac.cn\/biocode\/tools\/BT000004.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz008","type":"journal-article","created":{"date-parts":[[2019,1,8]],"date-time":"2019-01-08T10:41:10Z","timestamp":1546944070000},"page":"2949-2956","source":"Crossref","is-referenced-by-count":115,"title":["Characterization and identification of long non-coding RNAs based on feature relationship"],"prefix":"10.1093","volume":"35","author":[{"given":"Guangyu","family":"Wang","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences, Beijing, China"},{"name":"BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, China"},{"name":"University of Chinese Academy of Sciences , Beijing, China"}]},{"given":"Hongyan","family":"Yin","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences, Beijing, China"},{"name":"BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, China"},{"name":"University of Chinese Academy of Sciences , Beijing, China"}]},{"given":"Boyang","family":"Li","sequence":"additional","affiliation":[{"name":"Yale School of Public Health Department of Biostatistics, , New Haven, CT, USA"}]},{"given":"Chunlei","family":"Yu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences, Beijing, China"},{"name":"BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, China"},{"name":"University of Chinese Academy of Sciences , Beijing, China"}]},{"given":"Fan","family":"Wang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences, Beijing, China"},{"name":"BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, China"}]},{"given":"Xingjian","family":"Xu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences, Beijing, China"},{"name":"BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, China"},{"name":"University of Chinese Academy of Sciences , Beijing, China"}]},{"given":"Jiabao","family":"Cao","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences, Beijing, China"},{"name":"BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, China"},{"name":"University of Chinese Academy of Sciences , Beijing, China"}]},{"given":"Yiming","family":"Bao","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences, Beijing, China"},{"name":"BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2072-4826","authenticated-orcid":false,"given":"Liguo","family":"Wang","sequence":"additional","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine , Rochester, MN, USA"}]},{"given":"Amir A","family":"Abbasi","sequence":"additional","affiliation":[{"name":"National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University , Islamabad, Pakistan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5435-4750","authenticated-orcid":false,"given":"Vladimir B","family":"Bajic","sequence":"additional","affiliation":[{"name":"King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE) , Thuwal, Kingdom of Saudi Arabia"}]},{"given":"Lina","family":"Ma","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences, Beijing, China"},{"name":"BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, China"}]},{"given":"Zhang","family":"Zhang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences, Beijing, China"},{"name":"BIG Data Center, Beijing Institute of 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