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LncRNA的鉴定

长非编码RNA（lncRNA）是功能性非翻译分子，长度超过200个核苷酸，具有多种作用，例如染色质修饰，转录调控和蛋白质构象变化。 其实LncRNA并非严格意义的非编码RNA,越来越多的LncRNA被发现有sORF,编码少于100个氨基酸的微肽。

植物中的LncRNA数据库有：

GreeNC #包含常用的植物LncRNA的fasta序列，可以直接下载到本地使用。 [PlncRNADB][http://bis.zju.edu.cn/PlncRNADB/index.php] 支持物种少，拟南芥、玉米、毛果杨

LncRNA鉴定工具的综述 2020

LncRNA的预测：

植物LncRNA鉴定专用工具

  1. RNAplonc T.C. Negri, W.A.L. Alves, P.H. Bugatti, P.T.M. Saito, D.S. Domingues, A.R. Paschoal Pattern recognition analysis on long noncoding RNAs: a tool for prediction in plants Briefings in Bioinformatics’, 20 (2019), pp. 682-689
  2. CREMA C.M.A. Simopoulos, E.A. Weretilnyk, G.B. Golding Prediction of plant lncRNA by ensemble machine learning classifiers BMC Genomics, 19 (2018), p. 316
  3. PLIT S. Deshpande, J. Shuttleworth, J. Yang, S. Taramonli, M. England PLIT: An alignment-free computational tool for identification of long non-coding RNAs in plant transcriptomic datasets Comput Biol Med, 105 (2019), pp. 169-181
其他的LncRNA鉴定工具
  1. LGC（2019年发表） LGC用于预测LncRNA 动植物都可以使用 LGC的文章表明LGC的预测的鲁棒性和准确度要高于基于比对的算法 LGC基于ORF长度和GC含量之间的特征关系，与蛋白质编码RNA相比，来预测LncRNA
  2. CPC Kong L. et al. (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res., 35, W345–W349. (Web Server issue).
  3. COME Hu L. et al. (2017) COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features. Nucleic Acids Res., 45, e2.
  4. PhyloCSF Lin M.F. et al. (2011) PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics, 27, i275–i282.
简单的LncRNA测序分析文章

2020《BMC genomics》LncRNA

LncRNA和miRNA相互作用 综述 Veneziano D., Marceca G.P., Di Bella S., Nigita G., Distefano R., Croce C.M. (2019) Investigating miRNA–lncRNA Interactions: Computational Tools and Resources. In: Laganà A. (eds) MicroRNA Target Identification. Methods in Molecular Biology, vol 1970. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9207-2_14

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