Bilkent University
Department of Computer Engineering


Tandem Repeat Evolution in the Human Genome:
An Algorithmic Study

S. Cenk Şahinalp

Associate Professor,
School of Computing Science,
Simon Fraser University,
Burnaby BC, Canada

The human genome contains several classes of repeat segments such as common repeats, interspersed repeats, and tandem repeats, which, in total, cover more than 60% of the human genome sequence. Known mechanisms for the generation and propagation of genome repeats include unequal crossovers, replication slippage, and retrotransposition; there are potentially many more awaiting discovery.

In this talk, we propose the existence of an unknown mechanism partially responsible for the propagation of the alpha satellite DNA, the most common tandem repeat sequence in the human genome. This unknown mechanism seems to complement the unequal crossover events that were previously thought to be solely responsible for the generation and expansion of all satellite sequences.

The talk will focus on computational/algorithmic methods to collect, evaluate and analyze the sequence information from select regions of human centromeric DNA and will provide mathematical evidence that the unequal crossovers may not solely explain the composition of the alpha satellite sequences.

Joint work with Evan Eichler, Can Alkan and Eray Tuzun

DATE: April 27, 2004, Tuesday @ 16:40