The human genome is approximately 3 billion basepairs long. An estimated 2--3% of DNA codes for genes; the remaining 97--98% is noncoding DNA 11. Although the noncoding regions in DNA were once called "junk DNA" (with the assumption that these regions were not serving a purpose) it is now understood that within noncoding DNA are functional regions that affect the expression of genes 34. However, we are still far from understanding the breadth of function in the noncoding regions, and identification of functional elements is a complex problem, difficult to study in vitro because of the enormous number of possibilities. In this project, we are searching in silico for candidate functional elements in noncoding DNA. These candidates will then be studied at the bench to assess function. Our guiding principle is that regions of noncoding DNA that have been conserved across evolutionary time are good candidates as functional elements; we use a genetic algorithms approach to search for these candidate elements, called motifs. Our system is thus called GAMI, Genetic Algorithms for Motif Inference. GAMI has been demonstrated to be a successful approach to this task, as will be described below.
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It's not junk!: the search for functional elements in noncoding DNA
Congdon, Clare Bates; Gaskins, H. Rex; Nava, Gerardo M.; Mattingly, Carolyn
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, Volume 3 (3)
Association for Computing Machinery – Aug 1, 2008
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