The leading method for determining how transcription factors behave in living cells is to chop up the DNA from millions of cells and use protein antibodies to extract the fragments that have a particular transcription factor attached to them. While the DNA sequence that a transcription factor binds to consists of only about six to 12 DNA letters, the fragment extracted by the antibody could be a couple of hundred letters long. Sequencing the fragments can determine where in the genome they came from, but it offers little information about where on the fragment the transcription factor is attached.
David Gifford, a professor of electrical engineering and computer science and director of the Computational Genomics Group, his graduate student Yuchun Guo, and Shaun Mahony, a research scientist in the group, developed a new algorithm for analyzing millions of experimentally identified fragments and inferring the precise locations at which transcription factors bind to them. The rest of the article is available on MIT news.