2.1: Introduction

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Sequence alignment is a powerful tool capable of revealing the patterns and functions of genes. If two genetic regions are similar or identical, sequence alignment can demonstrate the conserved elements or differences between them. Evolution has preserved two broad classes of functional elements in the genome. Such pre- served elements between species are often homologs¹ – either orthologous or paralogous sequences (refer to Appendix 2.11.1). Both classes of conserved elements can help demonstrate the function or evolutionary history of a gene sequence. Primarily solved using computational methods (most frequently dynamic programming), sequence alignment is a fast and powerful way to find similarities among genes or genomes. These notes discuss the sequence alignment problem, the technique of dynamic programming, and a specific solution to the problem using this technique.

1 Homologous sequences are genomic sequences descended from a common ancestor.