Multiple sequence alignment

Punto Bawono, Maurits Dijkstra, Walter Pirovano, Anton Feenstra, Sanne Abeln, Jaap Heringa*

*Corresponding author for this work

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review


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.

Original languageEnglish
Title of host publicationBioinformatics
Subtitle of host publicationVolume I: Data, Sequence Analysis, and Evolution
EditorsJonathan M. Keith
PublisherHumana Press Inc
Number of pages23
ISBN (Electronic)9781493966226
ISBN (Print)9781493966202, 9781493982523
Publication statusPublished - 2017

Publication series

NameMethods in Molecular Biology
PublisherHumana Press
ISSN (Print)1064-3745


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


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