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Sequence Alignment

  • Xuhua Xia
Chapter

Abstract

Sequence alignment serves two purposes: global alignment is mainly for identifying site homology between sequences to facilitate the inference of ancestral-descendant relationships through molecular phylogenetics, and local alignment mainly for identifying sequence similarities that may be due to either inheritance or convergence. Dynamic programming algorithm for pairwise alignment and profile alignment is illustrated in detail, for both constant gap penalty and affine function gap penalty, followed by progressive multiple sequence alignment using a guide tree, and by how to align protein-coding nucleotide sequences against aligned amino acid sequences. Derivation of PAM and BLOSUM matrices were numerically illustrated in detail, and how the effect of purifying selection on substitution patterns is discussed. Also discussed are pros and cons of representing internal sequences by a profile or by a reconstructed sequence in multiple sequence alignment.

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Xuhua Xia
    • 1
  1. 1.University of Ottawa CAREG and Biology DepartmentOttawaCanada

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