A tandem repeat in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats occur in the genomes of both eukaryotic and prokaryotic organisms. They are important in numerous fields including disease diagnosis, mapping studies, human identity testing, sequence homology and population studies. Although tandem repeats have been used by biologists for many years, there are few tools available for performing an exhaustive search for all tandem repeats in a given sequence.

In this talk we present a new and interesting definition of approximate tandem repeats, based upon the concept of evolutive tandem repeats, and the edit distance measure. We then describe an efficient, deterministic algorithm for finding all such tandem repeats within a sequence. The algorithm has been implemented, and we have developed an online database that contains the tandem repeats found in the human genome. The database is available at http://tandem.sci.brooklyn.cuny.edu. This tool may assist biologists in discovering new ways that tandem repeats affect both the structure and function of DNA and protein molecules.

Bio:

Dr. Dina Sokol received her Ph.D. in Computer Science at Bar-Ilan University, Israel. Her research was supported by a grant from the Israel Ministry of Trade and Industry. Her postdoc at Bar-Ilan was funded by the Israel Science Foundation. She then spent six months as a researcher at AT&T Shannon Laboratory, New Jersey.

Dr. Sokol is currently an Associate Professor at Brooklyn College, Department of Computer and Information Science. Her research in Pattern Matching Algorithms spans the fields of computer science and computational biology. Currently, her research group is developing TRedD - a software tool and database for tandem repeats in DNA sequences, supported by the National Science Foundation.