生物信息学2025，Vol.23Issue(4)：323-329,7.DOI:10.12113/202409009
基于Linux系统构建lncRNA-seq生物信息学本地分析平台
Construction of localized lncRNA-seq bioinformatics analysis platform based on the Linux system
摘要
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.关键词
长非编码RNA/分析平台/Linux/生物信息学Key words
Long noncoding RNA/Analysis platform/Linux/Bioinformatics分类
生物科学引用本文复制引用
HUANG Pingping,WANG Jiarong,SHAN Yanan,ZHOU Bailing..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):323-329,7.基金项目
山东省自然科学基金青年项目(No.ZR2021QF143) （No.ZR2021QF143）
德州学院人才引进项目(No.2020xjrc216) （No.2020xjrc216）
德州学院横向课题(No.HXKT2023211) （No.HXKT2023211）
山东省教育厅高等学校人才引育计划. （）
