Multiple sequence alignment

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

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

Abstract

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 publicationMethods in Molecular Biology
Subtitle of host publicationVolume I: Data, Sequence Analysis, and Evolution
PublisherHumana Press Inc
Pages167-189
Number of pages23
Volume1525
DOIs
Publication statusPublished - 2017

Publication series

NameMethods in Molecular Biology
Volume1525
ISSN (Print)10643745

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Sequence Alignment
Sequence Analysis
Proteins
Nucleotides
Research Personnel

Keywords

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

Cite this

Bawono, P., Dijkstra, M., Pirovano, W., Feenstra, A., Abeln, S., & Heringa, J. (2017). Multiple sequence alignment. In Methods in Molecular Biology: Volume I: Data, Sequence Analysis, and Evolution (Vol. 1525, pp. 167-189). (Methods in Molecular Biology; Vol. 1525). Humana Press Inc. https://doi.org/10.1007/978-1-4939-6622-6_8
Bawono, Punto ; Dijkstra, Maurits ; Pirovano, Walter ; Feenstra, Anton ; Abeln, Sanne ; Heringa, Jaap. / Multiple sequence alignment. Methods in Molecular Biology: Volume I: Data, Sequence Analysis, and Evolution. Vol. 1525 Humana Press Inc, 2017. pp. 167-189 (Methods in Molecular Biology).
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Bawono, P, Dijkstra, M, Pirovano, W, Feenstra, A, Abeln, S & Heringa, J 2017, Multiple sequence alignment. in Methods in Molecular Biology: Volume I: Data, Sequence Analysis, and Evolution. vol. 1525, Methods in Molecular Biology, vol. 1525, Humana Press Inc, pp. 167-189. https://doi.org/10.1007/978-1-4939-6622-6_8

Multiple sequence alignment. / Bawono, Punto; Dijkstra, Maurits; Pirovano, Walter; Feenstra, Anton; Abeln, Sanne; Heringa, Jaap.

Methods in Molecular Biology: Volume I: Data, Sequence Analysis, and Evolution. Vol. 1525 Humana Press Inc, 2017. p. 167-189 (Methods in Molecular Biology; Vol. 1525).

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

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Bawono P, Dijkstra M, Pirovano W, Feenstra A, Abeln S, Heringa J. Multiple sequence alignment. In Methods in Molecular Biology: Volume I: Data, Sequence Analysis, and Evolution. Vol. 1525. Humana Press Inc. 2017. p. 167-189. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-6622-6_8