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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Multiple Sequence Alignment.

Punto Bawono¹, Maurits Dijkstra¹, Walter Pirovano²

¹Centre for Integrative Bioinformatics, Vrije Universiteit, Amsterdam, The Netherlands.

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

|November 30, 2016

Summary

This summary is machine-generated.

Next Generation Sequencing (NGS) advances underscore the importance of multiple sequence alignment (MSA) for analyzing biological sequences. This guide offers an overview of MSA methods for protein sequence alignment, aiding researchers in constructing reliable alignments.

Keywords:

Amino acid exchange matrix Dynamic programming Gap penalty Multiple sequence alignment Phylogenetic tree Progressive alignment Sequence profile

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Next Generation Sequencing (NGS) has increased the demand for effective multiple sequence alignment (MSA).
MSA is crucial for understanding biological sequence-structure-function relationships in protein and nucleotide families.
Despite advances, open biological and methodological challenges remain in MSA.

Purpose of the Study:

To provide background information on multiple sequence alignment (MSA) techniques.
To offer a practical overview of current MSA methods for protein sequence alignment.
To guide researchers in selecting and applying appropriate MSA tools.

Main Methods:

Review of existing literature and tools for multiple sequence alignment.
Focus on protein sequence alignment methodologies.
Analysis of advantages and limitations of various MSA approaches.

Main Results:

Identification of key considerations for performing MSA.
Categorization of available MSA tools with their respective strengths and weaknesses.
Discussion of unresolved biological and methodological issues in MSA.

Conclusions:

Reliable MSA is essential for comparative analysis of biological sequences.
Understanding different MSA methods is critical for accurate biological insights.
This chapter serves as a foundational resource for researchers undertaking MSA.