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Nowadays, many machine learning-based tools have been developed for lncRNA identification. However, many methods predict lncRNAs using sequence-derived features alone, which tend to display unstable performances on different species. Moreover, the majority of tools cannot be re-trained or tailored by users and neither can the features be customized or integrated to meet researchers\u2019 requirements. In this study, features extracted from sequence-intrinsic composition, secondary structure and physicochemical property are comprehensively reviewed and evaluated. An integrated platform named LncFinder is also developed to enhance the performance and promote the research of lncRNA identification. LncFinder includes a novel lncRNA predictor using the heterologous features we designed. Experimental results show that our method outperforms several state-of-the-art tools on multiple species with more robust and satisfactory results. Researchers can additionally employ LncFinder to extract various classic features, build classifier with numerous machine learning algorithms and evaluate classifier performance effectively and efficiently. LncFinder can reveal the properties of lncRNA and mRNA from various perspectives and further inspire lncRNA\u2013protein interaction prediction and lncRNA evolution analysis. It is anticipated that LncFinder can significantly facilitate lncRNA-related research, especially for the poorly explored species. LncFinder is released as R package (https:\/\/CRAN.R-project.org\/package=LncFinder). A web server (http:\/\/bmbl.sdstate.edu\/lncfinder\/) is also developed to maximize its availability.<\/jats:p>","DOI":"10.1093\/bib\/bby065","type":"journal-article","created":{"date-parts":[[2018,6,26]],"date-time":"2018-06-26T19:14:56Z","timestamp":1530040496000},"page":"2009-2027","source":"Crossref","is-referenced-by-count":150,"title":["LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property"],"prefix":"10.1093","volume":"20","author":[{"given":"Siyu","family":"Han","sequence":"first","affiliation":[{"name":"College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanchun","family":"Liang","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China"},{"name":"Zhuhai Laboratory of Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Zhuhai College of Jilin University, Zhuhai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3264-8392","authenticated-orcid":false,"given":"Qin","family":"Ma","sequence":"additional","affiliation":[{"name":"Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakot State University, Brookings, SD, USA"},{"name":"Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yangyi","family":"Xu","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Du","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cankun","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7804-149X","authenticated-orcid":false,"given":"Ying","family":"Li","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,7,31]]},"reference":[{"issue":"9","key":"2020011102320305900_bby065-B1","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1101\/gr.135350.111","article-title":"GENCODE: the reference human genome annotation for the ENCODE project","volume":"22","author":"Harrow","year":"2012","journal-title":"Genome Res"},{"issue":"9","key":"2020011102320305900_bby065-B2","doi-asserted-by":"crossref","first-page":"1775","DOI":"10.1101\/gr.132159.111","article-title":"The GENCODE v7 catalogue of human long non-coding RNAs: analysis of their structure, evolution and expression","volume":"22","author":"Derrien","year":"2012","journal-title":"Genome Res"},{"issue":"1","key":"2020011102320305900_bby065-B3","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1016\/j.cell.2013.06.009","article-title":"Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins","volume":"154","author":"Guttman","year":"2013","journal-title":"Cell"},{"issue":"7414","key":"2020011102320305900_bby065-B4","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nature11233","article-title":"Landscape of transcription in human cells","volume":"489","author":"Djebali","year":"2012","journal-title":"Nature"},{"issue":"6099","key":"2020011102320305900_bby065-B5","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1126\/science.337.6099.1159","article-title":"Genomics. 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