首页|Plant-LncPipe:a computational pipeline providing significant improvement in plant lncRNA identification

Plant-LncPipe:a computational pipeline providing significant improvement in plant lncRNA identification

扫码查看
原文链接
  • NETL
  • NSTL
  • 万方数据
Long non-coding RNAs(lncRNAs)play essential roles in various biological processes,such as chromatin remodeling,post-transcriptional regulation,and epigenetic modifications.Despite their critical functions in regulating plant growth,root development,and seed dormancy,the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods.Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets,and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited.To overcome this limitation,we retrained several models,including CPAT,PLEK,and LncFinder,using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2,CNCI,RNAplonc,and LncADeep.Retraining these models significantly improved their performance,and two of the retrained models,LncFinder-plant and CPAT-plant,alongside their ensemble,emerged as the most suitable tools for plant lncRNA identification.This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification.Finally,we developed a pipeline(Plant-LncPipe)that incorporates an ensemble of the two best-performing models and covers the entire data analysis process,including reads mapping,transcript assembly,lncRNA identification,classification,and origin,for the efficient identification of lncRNAs in plants.The pipeline,Plant-LncPipe,is available at:https://github.com/xuechantian/Plant-LncRNA-pipline.

Xue-Chan Tian、Zhao-Yang Chen、Shuai Nie、Tian-Le Shi、Xue-Mei Yan、Yu-Tao Bao、Zhi-Chao Li、Hai-Yao Ma、Kai-Hua Jia、Wei Zhao、Jian-Feng Mao

展开 >

State Key Laboratory of Tree Genetics and Breeding,National Engineering Research Center of Tree Breeding and Ecological Restoration,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design,National Engineering Laboratory for Tree Breeding,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants,Ministry of Education,College of Biological Sciences and Technology,Beijing Forestry University,Beijing 100083,China

Rice Research Institute,Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province),Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding,Guangzhou 510640,China

Key Laboratory of Crop Genetic Improvement & Ecology and Physiology,Institute of Crop Germplasm Resources,Shandong Academy of Agricultural Sciences,Jinan 250100,China

Department of Plant Physiology,Umeå Plant Science Centre(UPSC),Umeå University,Umeå 90187,Sweden

Department of Plant Physiology,Umeå Plant Science Centre(UPSC)

展开 >

国家重点研发计划国家自然科学基金

2022YFD220010332171816

2024

10.1093/hr/uhae041

园艺研究(英文)

园艺研究(英文)

CSTPCD
ISSN：
年,卷(期)：2024.11(4)
  • 31