We use DNA in biological research, such as J Robert Macey's work with reptiles and amphibians. Specimens are collected and tissue samples are taken, snap-frozen in LN₂ (liquid nitrogen), then stored in our -80°C freezers.

When we are ready to work with our samples we extract the DNA. We can then amplify with PCR to create many copies of a specific gene. However, there are other ways we can work with the DNA to create an entire genomic library, such as molecular cloning using bacteria.

Libraries are fragments of DNA which are cloned and stored using bacteria. The clones vary in size:

BAC and Fosmid clones are large-insert clones, while plasmids are small-insert clones. Using the clones of various sizes, we can assemble an entire genome with utilizing paired-end reads.

We can store our DNA inside of bacterial artificial chromosomes, or BAC libraries. Plasmids are small, circular, double-stranded segments of DNA that are not part of the bacterial chromosome. They are transmitted from one bacteria to others through conjugation, resulting in horizontal gene transfer. This allows advantageous genes to propogate. Molecular cloning utilizes this same process.

Fosmids are used for creating mini-BAC libraries of specific chromosomes.

Plasmid clones are small-insert clones used to create contigs.

Contigs are sets of overlapping DNA fragments which, when combined together, create a complete sequence of DNA for a particular region of the genome.

Contigs assembly is assisted with paired-end reads from inserts of known size in plasmid clones.

Shotgun sequencing is a strategy for assembly of random segments in a genome.

Contig assemblies assisted with paired-end readings are used to create a scaffold based on paired-end readings.

Analyzing the assembled genome, we can generate trees to determine how species are related.