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An overview of multiple sequence alignment.

Victor Simossis1, Jens Kleinjung1, Jaap Heringa1

  • 1Integrative Bioinformatics Institute (IBIVU), Free University, Amsterdam, The Netherlands.

Current Protocols in Bioinformatics
|April 23, 2008
PubMed
Summary
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Multiple sequence alignment (MSA) is a key bioinformatics method for understanding biological sequences. This overview covers 30 years of MSA techniques, their challenges, and evaluation.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Multiple sequence alignment (MSA) is a foundational bioinformatics technique.
  • MSA provides critical insights into sequence-structure-function relationships for nucleotide and protein families.

Purpose of the Study:

  • To provide a comprehensive overview of multiple sequence alignment techniques.
  • To trace the historical development of MSA from early methods to current state-of-the-art approaches.
  • To discuss associated methodological, biological, and evaluation challenges.

Main Methods:

  • Review of historical development of multiple sequence alignment algorithms.
  • Discussion of current state-of-the-art multiple sequence alignment techniques.
  • Analysis of biological and methodological considerations in sequence alignment.

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Main Results:

  • The field of multiple sequence alignment has evolved significantly over the past three decades.
  • Current techniques offer advanced capabilities for analyzing sequence families.
  • Key challenges in alignment accuracy, biological interpretation, and evaluation persist.

Conclusions:

  • Multiple sequence alignment remains an indispensable tool in bioinformatics.
  • Understanding the evolution and challenges of MSA is crucial for biological discovery.
  • Effective evaluation of alignment quality is essential for reliable biological insights.