Several approaches are available for identifying genes within a large, unsequenced DNA region. One method is the exon trap, which employs a specialized vector to selectively clone exons. Another involves using methylation-sensitive restriction enzymes to locate CpG islands—DNA regions containing unmethylated CpG sequences. Prior to the genomics era, geneticists mapped the Huntington disease gene (HD) to a region near the end of chromosome 4, subsequently using an exon trap to identify the gene itself.

Advancements in automated DNA sequencing methods have enabled molecular biologists to determine the base sequences of various organisms, from simple phages and bacteria to yeast, plants, animals, and humans. In the Human Genome Project, much of the mapping work utilized yeast artificial chromosomes (YACs), which are vectors containing a yeast origin of replication, a centromere, and two telomeres. These vectors can accommodate foreign DNA up to 1 million base pairs long, which replicates alongside the YAC. However, due to their superior stability and ease of use, bacterial artificial chromosomes (BACs) became the preferred tool for sequencing. BACs, derived from the F plasmid of E. coli, can accept DNA inserts up to approximately 300 kilobases, with an average insert size of about 150 kilobases.

Mapping large genomes, such as the human genome, requires a set of landmarks (markers) to determine the positions of genes. While genes themselves can serve as markers, most markers consist of anonymous DNA segments like RFLPs, VNTRs, STSs (including ESTs), and microsatellites. Restriction fragment length polymorphisms (RFLPs) are variations in the lengths of DNA fragments produced by cutting DNA from different individuals with a restriction enzyme, often caused by the presence or absence of specific restriction sites.