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Chapter

Cover Concepts in Bioinformatics and Genomics

Pairwise Sequence Alignment  

This chapter focuses on amino acid substitution matrices and pairwise sequence comparison programs. It begins by discussing the nuts and bolts of algorithms that use data from evolution and protein domain conservation to infer whether two genes are homologs. The chapter then explores the details of how pairwise sequence alignment is performed by computer programs originally written in the 1970s and 1980s and gradually improved. To approach the pairwise sequence alignment programs, the chapter first discusses the sliding window. The sliding window accumulates information or data about the properties of a segment of amino acid residues in a window of specific length within a long polypeptide. It then investigates how the sliding window program is used to create dot plots. Next, the chapter delves into the Needleman-Wunsch global alignment program and the Smith-Waterman local alignment program. It also considers the two updated versions of the Needleman-Wunsch global alignment programs.

Chapter

Cover Introduction to Genomics

Evolution and Genomic Change  

This chapter focuses on the coordination of changes in genotype and phenotype during evolution. It considers evolution to be an exploration that leads to discovery and change. It expounds on the principles of biological classification and the grammar of biological nomenclature, citing the biological taxonomy used for identifying different life forms. It differentiates between similarity and homology as well. It shows the measurements of similarities between gene or protein sequences amongst different species. The chapter explains the construction and calculation of phylogenetic trees, which are diagrams showing ancestor–descendant relationships. The chapter includes a description of the general idea of pattern recognition and introduces tools used in an effort to recognize similarities among sequences. It lists types of pattern matching, which is a basic tool of bioinformatics, such as dot plot and the BLOSUM62 matrix.

Chapter

Cover Introduction to Bioinformatics

Alignments and phylogenetic trees  

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.