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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Multiple alignment of DNA sequences with MAFFT.

Kazutaka Katoh¹, George Asimenos, Hiroyuki Toh

¹Digital Medicine Initiative, Kyushu University, Fukuoka, Japan.

Methods in Molecular Biology (Clifton, N.J.)

|April 21, 2009

Summary

This summary is machine-generated.

Multiple sequence alignment (MSA) programs like MAFFT are crucial for analyzing vast DNA sequence data. This chapter details MAFFT algorithms and offers practical guidance, introducing TBA and MAUVE for genome-scale alignments.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Multiple sequence alignment (MSA) is fundamental for molecular biology analyses.
Increasingly large datasets from sequencing projects necessitate scalable and accurate MSA tools.

Purpose of the Study:

To outline the algorithms of the MAFFT multiple sequence alignment program.
To provide practical advice for biologists using MSA tools in typical scenarios.
To introduce alternative tools (TBA, MAUVE) for genome-scale alignment tasks.

Main Methods:

Detailed explanation of MAFFT algorithms.
Practical guidance for MSA application in biological research.
Introduction to TBA and MAUVE for large-scale genome alignments.

Main Results:

MAFFT offers scalable and accurate multiple sequence alignment capabilities.
Specific advice is provided for common challenges faced by biologists.
TBA and MAUVE are presented as solutions for genome alignment.

Conclusions:

MAFFT is a valuable tool for DNA sequence alignment, balancing accuracy and scalability.
Biologists can effectively utilize MAFFT with practical guidance.
Specialized tools are recommended for genome-wide alignment challenges.