This technique of sequencing, however, has two major shortcomings. The length of the DNA being sequenced cannot be longer than 1000 base pairs long, or it will be completely inaccurate. Typically, sequencing is done on strands of DNA no longer than 850 base pairs long for the best accuracy. This has severe implications for the sequencing of large genomes such as humans, which have a genome of almost 3 billion base pairs!. In addition, this technique of sequencing has another major flaw that one can see from the image above: it requires that the sequences be read by a person. The amount of time it would take for people to manually read and record genomes billions of base pairs long would be impractical for realistic research.

The invention of automated sequencers in 1987 by Applied Biosystems was a breakthrough in the ability of geneticists to sequence large genomes. While the limitation of 1000 base pairs for sequencing is still unavoidable, it solves the problem of needing people to read and record the sequence. In an automated sequencing process, instead of labelling the primers with radioactive labels, the ddNTP is labeled with a fluorescent label, where each ddNTP would fluoresce a different color when a laser is fired through it. Unlike the autoradiography, which will show a band of the same color regardless of the ddNTP, this method will fluoresce a different color for each of the four different nucleotides. Thus, this allows for the sequencing reaction to occur in one tube, as each ddNTP would fluoresce a different color and identify the nucleotide in the sequence. Once the reaction was ran to completion, it was placed into a gel tray where an electric current would be applied from the tray into 96 microcapillaries, all of which will gather at a laser. The idea is that the DNA will migrate towards the positive electrode at the laser end, where it would fluoresce a specific wavelength of light once the DNA passes through, and get recorded by a computer detector. The wavelength of light detected would be automatically associated with the corresponding nucleotide, allowing computers to automatically print out a chromatogram as well as the sequence, similar to this image: