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Related Experiment Video

Updated: Mar 8, 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

MARS: improving multiple circular sequence alignment using refined sequences.

Lorraine A K Ayad¹, Solon P Pissis²

¹Department of Informatics, King's College London, Strand, London, WC2R 2LS, UK.

|January 16, 2017

Summary

This summary is machine-generated.

This study introduces MARS, a method to improve multiple sequence alignment for circular DNA by optimizing sequence rotation. MARS refines sequence starting points, enhancing alignment accuracy and phylogenetic inference for biological sequence analysis.

Keywords:

Circular sequences Multiple circular sequence alignment Progressive alignment q-grams

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Last Updated: Mar 8, 2026

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

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Published on: March 10, 2020

Identification of Circular RNAs using RNA Sequencing

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Published on: November 14, 2019

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Multiple sequence alignment (MSA) assumes fixed start/end points, which is problematic for circular DNA due to arbitrary linearization.
Inconsistencies in sequence databases arise from differing linearization standards, affecting MSA accuracy.
Circular genomes like mitochondrial DNA, viral, and viroid genomes present unique challenges for standard MSA.

Purpose of the Study:

To address the limitations of conventional MSA for circular sequences with arbitrary start/end points.
To develop a method that can refine sequences before MSA, improving alignment quality.
To enhance the accuracy and efficiency of analyzing biological sequences with circular structures.

Main Methods:

Developed MARS (Multiple circular sequence Alignment using Refined Sequences), a heuristic method implemented in C++.
MARS computes optimal rotations (cyclic shifts) for each input sequence.
The refined sequences are then used with standard MSA programs.

Main Results:

MARS significantly improves multiple sequence alignments and subsequent maximum-likelihood-based phylogenies.
Experimental results on real and synthetic data demonstrate MARS outperforms state-of-the-art methods in accuracy and efficiency.
Applied to mitochondrial DNA, MARS reduced average pairwise distance in MSA by approximately 5%.

Conclusions:

MARS offers an effective and efficient solution for MSA of sequences with arbitrary starting positions.
The method is compatible with any existing multiple sequence alignment program.
Improved MSA through MARS enhances biological sequence analysis, particularly for circular genomes.