Related Experiment Video
Updated: Nov 25, 2025
Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
Published on: July 9, 2021
Classification of Long Noncoding RNAs by k-mer Content
Jessime M Kirk1,2,3,4, Daniel Sprague1,3,5,6, J Mauro Calabrese7,8,9,10
1Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Abstract:
K-mer based comparisons have emerged as powerful complements to BLAST-like alignment algorithms, particularly when the sequences being compared lack direct evolutionary relationships. In this chapter, we describe methods to compare k-mer content between groups of long noncoding RNAs (lncRNAs), to identify communities of lncRNAs with related k-mer contents, to identify the enrichment of protein-binding motifs in lncRNAs, and to scan for domains of related k-mer contents in lncRNAs. Our step-by-step instructions are complemented by Python code deposited in Github. Though our chapter focuses on lncRNAs, the methods we describe could be applied to any set of nucleic acid sequences.
Related Concept Videos
02:39lncRNA - Long Non-coding RNAs
02:39lncRNA - Long Non-coding RNAs
03:21RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
02:53Ribosomal RNA Synthesis
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
01:20Types of RNA
RNA Performs Diverse...
01:23Types of RNA
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...