Show Summary Details
Introduction to Bioinformatics

Introduction to Bioinformatics

Arthur M. Lesk
Page of

Printed from Oxford Science Trove. Under the terms of the licence agreement, an individual user may print out a single article for personal use (for details see Privacy Policy and Legal Notice).

date: 24 June 2024

4. Alignments and phylogenetic treeslocked

4. Alignments and phylogenetic treeslocked

  • Arthur M. LeskArthur M. LeskThe Pennsylvania State University

Abstract

This chapter examines the concept of sequence alignment, which is the identification of residue-residue correspondences. It is the basic tool of bioinformatics. The chapter presents a comparison of pairwise sequence alignments and multiple sequence alignments. Multiple sequence alignments are much more informative than pairwise sequence alignments, in terms of revealing patterns of conservation. The chapter then looks at the process of constructing and interpreting dot plots, before considering the use of the Hamming distance and Levenshtein distance as measures of dissimilarity of character strings. It also explains the basis of scoring schemes for string alignment, including substitution matrices and gap penalties. Finally, the chapter studies the applications of multiple sequence alignments to database searching, before exploring the contents and significance of phylogenetic trees, and the methods available for deriving them.

You do not currently have access to this article

Login

Please login to access the full content.

Subscribe

Access to the full content requires a subscription