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RNA Editing

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...

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Updated: Jun 2, 2026

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

Boulder ALignment Editor (ALE): a web-based RNA alignment tool.

Jesse Stombaugh¹, Jeremy Widmann, Daniel McDonald

¹Department of Chemistry and Biochemistry, University of Colorado, CO, USA.

Bioinformatics (Oxford, England)

|May 7, 2011

Summary

This summary is machine-generated.

The Boulder ALignment Editor (ALE) is a new web-based tool for RNA structure-informed alignments. It addresses the growing need for aligning non-coding RNA sequences and structures effectively.

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Area of Science:

Structural Biology
Bioinformatics
Computational Biology

Background:

Rapid advancements in RNA X-ray crystallography and whole-genome sequencing have led to a surge in RNA structural and sequence data.
Existing RNA alignment tools primarily focus on primary sequences, with limited support for structural information.

Purpose of the Study:

To develop a user-friendly, web-based tool for creating and assessing RNA alignments that incorporate structural data.
To address the limitations of current software in handling the influx of both sequence and structural information for non-coding RNAs.

Main Methods:

Development of the Boulder ALignment Editor (ALE), a web-based RNA alignment editor.
Implementation of features for annotating and evaluating alignments based on Watson-Crick and non-Watson-Crick base pair isostericity.
Inclusion of alignment collapsing (horizontal and vertical) while preserving editability.

Main Results:

ALE provides a novel approach to RNA alignment by integrating structural information.
The tool facilitates the annotation and evaluation of base pair isostericity within alignments.
ALE allows for flexible manipulation of alignments, including collapsing, while maintaining editing capabilities.

Conclusions:

The Boulder ALignment Editor (ALE) meets the urgent need for tools that can produce structure-informed RNA alignments.
ALE enhances the analysis of non-coding RNA by leveraging both sequence and structural data.
This tool supports researchers in the growing field of RNA structural biology and bioinformatics.