What Is a Genome?

A genome is the complete set of DNA in an organism. DNA, short for deoxyribonucleic acid, is the molecule that stores the instructions a cell uses to build and run itself. When we say the human genome or the E. coli genome, we mean every letter of DNA that organism carries, taken together as one full instruction manual.

The DNA Double Helix

DNA is a long chain built from four chemical building blocks called bases, written with the letters A, T, G, and C (adenine, thymine, guanine, and cytosine). Two of these chains twist around each other into the famous shape called the double helix. The chains are held together because the bases pair up in a fixed way: A always pairs with T, and G always pairs with C. Each of these matched rungs is called a base pair, and the base pair is the smallest unit we use to measure a genome.

Packaging Into Chromosomes

If you stretched out all the DNA from a single human cell end to end, it would be about two meters long, far too long to fit inside a microscopic cell. To solve this, the DNA is wound tightly around proteins and folded into compact bundles called chromosomes. A human cell packages its genome into 46 chromosomes, arranged as 23 pairs. A bacterium like E. coli is simpler and keeps its whole genome on a single circular chromosome. Either way, the genome is the sum of all the DNA across all of those chromosomes.

Because genomes contain enormous numbers of base pairs, we use shorthand units throughout this course. A kilobase (kb) is 1,000 base pairs, a megabase (Mb) is 1,000,000 base pairs, and a gigabase (Gb) is 1,000,000,000 base pairs. To feel how counting works on a tiny scale, we can count the letters in a short DNA sequence directly in the terminal. In the command below, printf prints the sequence without adding a line break, the vertical bar (called a pipe) hands that text to the next command, and wc -c counts how many characters there are (here, one byte per DNA letter). A line starting with # is a comment that the shell ignores.

# Count the number of bases (letters) in a short DNA sequence
printf 'ATGCGTACGTTAGC' | wc -c

# Convert the human genome size from base pairs to megabases
echo $((3200000000 / 1000000))

14
3200

The first number, 14, is the count of bases in that little sequence. The second command uses $(( )), which is how bash does arithmetic, to divide the human genome size by one million and show it in megabases. One thing to know is that bash only works with whole numbers, so this kind of division rounds down and throws away any leftover fraction; here 3,200,000,000 divides evenly by one million, so nothing is lost and it reports 3200. That means the human genome of roughly 3,200,000,000 base pairs is about 3,200 Mb, which is the same as 3.2 Gb. By comparison, the E. coli genome is only about 4.6 Mb, so a human carries hundreds of times more DNA than this common bacterium.

Genomics Versus Genetics

Classical genetics studies individual genes and how single traits are passed from parents to offspring, often one gene at a time. Genomics zooms out to study the entire genome at once, using computers to read, store, and compare millions or billions of base pairs. This course focuses on genomics: over the coming lessons you will learn how genomes are sequenced, how that data is stored in standard file formats, and how to use command line tools to explore real DNA sequences yourself.