Related Experiment Video
Updated: Jan 26, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
Bioinformatics Approaches to Studying Plant Long Noncoding RNAs (lncRNAs): Identification and Functional
Hai-Xi Sun1, Nam-Hai Chua2,3
1Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, USA.
Abstract:
Long noncoding RNAs (lncRNAs) play important roles in regulating various biological processes including growth and stress responses in plants. RNA-seq data sets provide a good resource to exploring the noncoding transcriptome and studying their comprehensive interactions with the coding transcriptome. Here, we describe computational procedures for studying plant lncRNAs including long intergenic noncoding RNAs (lincRNAs) and long noncoding natural antisense transcripts (lncNATs). Bioinformatics tools for transcriptome assembly, lncRNA identification, and functional interpretations are included. Finally, we also introduce PLncDB, a user-friendly database that provides comprehensive information of plant lncRNAs for researchers to compare their own data sets to those in public database.
Related Concept Videos
lncRNA - Long Non-coding RNAs
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Bioequivalence Data: Statistical Interpretation
siRNA - Small Interfering RNAs
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the...
Design Example: Setting a Curve Using Design Data
piRNA - Piwi-interacting RNAs

