This part of the book deals with some of the fundamental operations in bioinformatics. We learn how to access different kinds of molecular data (such as protein and DNA sequences) in Chapter 2. We perform pairwise alignment in Chapter 3, and then search a query (such as a protein or DNA sequence) against an entire database using BLAST in Chapter 4. In Chapter 5 we examine advanced techniques for searching databases, such as the sensitive DELTA-BLAST algorithm for searching protein databases using position-specific scoring matrices, and specialized methods for searching genomic DNA databases. We extend the alignment problem to multiple sequences in Chapter 6, and we visualize multiple sequence alignments using the tools of phylogeny in Chapter 7. That chapter also introduces principles of molecular evolution.