types is usually involved. If a fl uorescent molecule is attached to the added bases, the color signal it gives off can be seen using optical microscopy. Fluorescence detection is employed in both base-extension and ligation sequencing by many groups, including those of Michael Metzker and his colleagues at Baylor University, Robi Mitra of Washington University in St. Louis, my own lab at Harvard Medical School and at Agencourt Bioscience Corporation. An alternative method uses bioluminescent proteins, such as the fi refl y enzyme luciferase, to detect pyrophosphate released when a base attaches to the primer strand. Developed by Mostafa Ronaghi, who is now at Stanford University, this system is used by Pyrosequencing/Biotage and 454 Life Sciences. Both forms of detection usually require multiple instances of the matching reaction to happen at the same time to produce a signal strong enough to be seen, so many copies of the sequence of interest are tested simultaneously. Some investigators, however, are working on ways to detect fl uorescent signals emitted from just one template strand molecule. Stephen Quake of the California Institute of Technology and scientists at Helicos Biosciences and Nanofl uidics are all taking this single-molecule approach, intended to save time and costs by eliminating the need to make copies of the template to be sequenced.