title: Multiple Sequence Alignment.
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.
authors.affiliation: Centre for Integrative Bioinformatics, Vrije Universiteit, Amsterdam, The Netherlands.
authors.forename: Punto
authors.initials: P
authors.lastname: Bawono
authors.affiliation: Centre for Integrative Bioinformatics, Vrije Universiteit, Amsterdam, The Netherlands.
authors.forename: Maurits
authors.initials: M
authors.lastname: Dijkstra
authors.affiliation: Bioinformatics Department, BaseClear, Leiden, The Netherlands.
authors.forename: Walter
authors.initials: W
authors.lastname: Pirovano
authors.affiliation: Centre for Integrative Bioinformatics, Vrije Universiteit, Amsterdam, The Netherlands.
authors.forename: Anton
authors.initials: A
authors.lastname: Feenstra
authors.affiliation: Centre for Integrative Bioinformatics, Vrije Universiteit, Amsterdam, The Netherlands.
authors.forename: Sanne
authors.initials: S
authors.lastname: Abeln
authors.affiliation: Centre for Integrative Bioinformatics, Vrije Universiteit, Amsterdam, The Netherlands. heringa@cs.vu.nl.
authors.forename: Jaap
authors.initials: J
authors.lastname: Heringa
mesh_terms: D000465:Algorithms; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins
keywords: Amino acid exchange matrix; Dynamic programming; Gap penalty; Multiple sequence alignment; Phylogenetic tree; Progressive alignment; Sequence profile