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Updated: Jan 27, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures.

Rafael C A Tavares¹, Anna Marie Pyle², Srinivas Somarowthu³

¹Department of Chemistry, Yale University, New Haven, CT 06511, USA.

Journal of Molecular Biology

|March 21, 2019

Summary

Researchers enhanced R-scape, a tool for RNA structure analysis. This adaptation improves the identification of conserved RNA structures in long molecules like mammalian long non-coding RNAs (lncRNAs).

Keywords:

RNAalifold conserved structure covariation analysis lncRNA structure long non-coding RNAs

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Area of Science:

Molecular Biology
Bioinformatics
Evolutionary Biology

Background:

Evolutionary conservation of RNA base pairing suggests functional structural elements.
Existing tools for identifying RNA structural conservation have limitations, particularly for long or eukaryotic RNAs.
R-scape is a pairwise covariation analysis tool with initial limitations on long RNA sequences.

Purpose of the Study:

To adapt and enhance the R-scape program for more powerful analysis of RNA structure conservation.
To improve the identification of conserved structural elements in long RNA molecules, including mammalian lncRNAs.

Main Methods:

Statistical prediction of pairwise covariation from sequence alignments.
Adaptation of the R-scape program for analyzing long RNA molecules.
Application of the enhanced R-scape to mammalian long non-coding RNAs (lncRNAs).

Main Results:

Demonstrated successful adaptation of R-scape for analyzing long RNAs.
Showcased improved utility of R-scape for structure conservation in eukaryotic RNAs.
Successfully applied the method to identify conserved structures in mammalian lncRNAs.

Conclusions:

The adapted R-scape program offers a more powerful approach for studying RNA structure conservation.
This enhancement is particularly valuable for analyzing long and complex RNA molecules like lncRNAs.
The findings facilitate a deeper understanding of functional RNA structures in mammals.