Introduction Genomics DNA is the fundamental encoding of the instructions that govern the operation of living cells and by extension, biological organisms. You can think of DNA as a storage medium in which the pro- gram that executes within all of your cells is written. The "machine code" of DNA, corresponding to the byte-code of Java, consists of only four nucleotides: four amino acids that are arranged in a linear sequence along the DNA molecule. These four bases are: guanine (G, adenine (A), thymine (T), and cytosine (C). So, a DNA molecule can be represented as a string made up of those four letters. The science of bioinformatics is largely concerned with computations on such genetic strings, or sequences. There are a variety of computations that one might perform on genetic sequences. We will investigate two types: basic statistics of individual sequences and pairwise alignments used to compare pairs of sequences