| 引用本文: | 黄平平,王佳容,单亚男,周百灵.基于Linux系统构建lncRNA-seq生物[]信息学本地分析平台[J].生物信息学,2025,23(4):323-329. |
| HUANG Pingping,WANG Jiarong,SHAN Yanan,ZHOU Bailing.Construction of localized lncRNA-seq bioinformatics analysisplatform based on the Linux system[J].Chinese Journal of Bioinformatics,2025,23(4):323-329. |
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| 摘要: |
| 长非编码RNA(Long noncoding RNA, lncRNA)是一类转录本长度大于200 nt、缺乏蛋白质编码能力的RNA分子,可通过与mRNA、蛋白质和miRNA等分子相互作用从而以多种形式在不同水平调控基因表达。近年来,lncRNA在人类疾病发生发展、动物生长发育和植物应对环境胁迫等方面的研究一直是国内外研究热点和持续关注的焦点。目前,关于人类、动植物lncRNA的研究主要采用lncRNA测序(lncRNA-sequencing, lncRNA-seq)的方法。lncRNA-seq数据的分析依赖众多软件,且大部分是在Linux系统通过命令行的方式运行,对于大多数研究者开展数据分析可能存在困难。因此,文中在调研现有的lncRNA-seq数据分析流程的基础上,基于Linux系统构建lncRNA-seq本地分析平台,平台主要包括以下几个步骤:首先采用trimmomatic对原始测序数据进行质量控制,使用软件Hisat2和StringTie进行序列的比对、组装,通过Salmon软件进行转录本的定量,结合CPC2、CNCI、Pfam 和PLEK对新的转录本进行编码能力预测。另外,以2组马铃薯测序数据为例详细介绍数据分析过程,以便同领域研究者在服务器上构建本地化分析平台、灵活地开展数据分析。 |
| 关键词: 长非编码RNA 分析平台 Linux 生物信息学 |
| DOI：10.12113/202409009 |
| 分类号:Q52 |
| 文献标识码:A |
| 基金项目:山东省自然科学基金青年项目(No.ZR2021QF143);德州学院人才引进项目(No.2020xjrc216);德州学院横向课题(No.HXKT2023211);山东省教育厅高等学校人才引育计划. |
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| Construction of localized lncRNA-seq bioinformatics analysisplatform based on the Linux system |
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HUANG Pingping, WANG Jiarong, SHAN Yanan, ZHOU Bailing
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(Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, Shandong,China)
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| Abstract: |
| Long noncoding RNA (lncRNA) is a type of transcript with length longer than 200 nt and lacks protein coding ability. It can regulate the gene expression in various forms at different levels by interacting with mRNA, protein, and miRNA. In recent years, the studies of lncRNA in the occurrence and development of human diseases, animal growth and development, and plant response to environmental stress have attracted considerable attention. At present, the researches on the human, animal and plants lncRNAs are mainly performed based on the lncRNA-sequencing (lncRNA-seq) method. However, the analysis of lncRNA-seq data depends on many software and most of them are run in the Linux system, which might be difficult for most of researchers. Therefore, the paper investigates the existing lncRNA-seq data analysis process and constructs the localized lncRNA-seq analysis platform based on the Linux system. The platform mainly includes the following steps: first, the quality of the original sequencing data is controlled by the trimmomatic software and obtain the clean data; then, the clean data are mapped to the reference genome by hisat2 and the transcripts are assembled by stringtie; further, the quantification of the transcript is performed by salmon; the coding ability of the new transcript is predicted by four software, including CPC2, CNCI, Pfam and PLEK. In addition, two groups of potato sequencing data are taken as an example to introduce the data analysis process in detail, which can help the related researchers build a localized analysis platform on the server and carry out data analysis flexibly. |
| Key words: Long noncoding RNA Analysis platform Linux Bioinformatics |
