Bioinformatics pp 167-189 | Cite as

Multiple Sequence Alignment

  • Punto Bawono
  • Maurits Dijkstra
  • Walter Pirovano
  • Anton Feenstra
  • Sanne Abeln
  • Jaap HeringaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1525)


The increasing importance of Next Generation Sequencing (NGS) techniques has highlighted the key role of multiple sequence alignment (MSA) in comparative structure and function analysis of biological sequences. MSA often leads to fundamental biological insight into sequence–structure–function relationships of nucleotide or protein sequence families. Significant advances have been achieved in this field, and many useful tools have been developed for constructing alignments, although many biological and methodological issues are still open. This chapter first provides some background information and considerations associated with MSA techniques, concentrating on the alignment of protein sequences. Then, a practical overview of currently available methods and a description of their specific advantages and limitations are given, to serve as a helpful guide or starting point for researchers who aim to construct a reliable MSA.

Key words

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


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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Punto Bawono
    • 1
  • Maurits Dijkstra
    • 1
  • Walter Pirovano
    • 2
  • Anton Feenstra
    • 1
  • Sanne Abeln
    • 1
  • Jaap Heringa
    • 1
    Email author
  1. 1.Centre for Integrative BioinformaticsVrije UniversiteitAmsterdamThe Netherlands
  2. 2.Bioinformatics DepartmentBaseClearLeidenThe Netherlands

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