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They have important functions in cell development and metabolism, such as genetic markers, genome rearrangements, chromatin modifications, cell cycle regulation, transcription and translation. Their functions are generally closely related to their localization in the cell. Therefore, knowledge about their subcellular locations can provide very useful clues or preliminary insight into their biological functions. Although biochemical experiments could determine the localization of lncRNAs in a cell, they are both time-consuming and expensive. Therefore, it is highly desirable to develop bioinformatics tools for fast and effective identification of their subcellular locations.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed a sequence-based bioinformatics tool called \u2018iLoc-lncRNA\u2019 to predict the subcellular locations of LncRNAs by incorporating the 8-tuple nucleotide features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution approach. Rigorous jackknife tests have shown that the overall accuracy achieved by the new predictor on a stringent benchmark dataset is 86.72%, which is over 20% higher than that by the existing state-of-the-art predictor evaluated on the same tests.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>A user-friendly webserver has been established at http:\/\/lin-group.cn\/server\/iLoc-LncRNA, by which users can easily obtain their desired results.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty508","type":"journal-article","created":{"date-parts":[[2018,6,19]],"date-time":"2018-06-19T19:24:19Z","timestamp":1529436259000},"page":"4196-4204","source":"Crossref","is-referenced-by-count":259,"title":["iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC"],"prefix":"10.1093","volume":"34","author":[{"given":"Zhen-Dong","family":"Su","sequence":"first","affiliation":[{"name":"Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhao-Yue","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya-Wei","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"},{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"},{"name":"Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China"},{"name":"Gordon Life Science Institute, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kuo-Chen","family":"Chou","sequence":"additional","affiliation":[{"name":"Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"},{"name":"Gordon Life Science Institute, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Lin","sequence":"additional","affiliation":[{"name":"Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"},{"name":"Gordon Life Science Institute, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,6,21]]},"reference":[{"key":"2023012712261383900_bty508-B1","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1186\/1471-2199-11-99","article-title":"A thymus-specific noncoding RNA, Thy-ncR1, is a cytoplasmic riboregulator of MFAP4 mRNA in immature T-cell lines","volume":"11","author":"Aoki","year":"2010","journal-title":"BMC Mol. 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Rep"},{"key":"2023012712261383900_bty508-B112","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1093\/bioinformatics\/btx670","article-title":"PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy","volume":"34","author":"Song","year":"2018","journal-title":"Bioinformatics"},{"key":"2023012712261383900_bty508-B113","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.jtbi.2018.01.023","article-title":"PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural and network features in a machine learning framework","volume":"443","author":"Song","year":"2018","journal-title":"J. Theor. 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