CS Seminar, John Karro (Univ. of Miami Ohio): The identification and analysis of genomic transposable elements.

Tuesday, November 11, 2014
4:15 PM - 5:30 PM (ET)
ESC 638
Event Type
Academic Calendar
Contact
Janet Burge (jburge@wesleyan.edu)
Department
Math/CS Computer Science Seminar
Link
https://eaglet.wesleyan.edu/MasterCalendar/EventDetails.aspx?EventDetailId=63356

Abstract: Transposable Elements, or TEs, are mobile DNA sequences capable of inserting multiple copies of themselves into a genome. Throughout our evolutionary history the human genome has been repeatedly subjected to such insertions, to the point where upward of 45% of our genetic sequence is the remnants of TEs and other repetitive sequences. Identifying these TEs could be easily framed as a basic string-matching problem, were it not for the effect of genetic mutations: while a given TE was initially a copy of its progenitor sequence, over time the DNA sequence changed in an apparently random manner. Thus the identification problem becomes significantly more difficult, and is even further complicated by size of the input which any solution algorithm will be applied. Given the size of the higher-order genomes (e.g. n ≈ 3?109 for human, n ≈ 5x1010 for salamander), any identification algorithm must have runtime and memory usage bounds that scale linearly with input size if the algorithm is to be of practical use. But once TEs have been identified, they provide important information on the very mutation rates that made them so hard to identify ? giving us a window into genomic evolutionary history. This talk will explore how and why we are solving the identification problem. We will describe the algorithm underlying RAIDER, a new tool for the fast de novo identification of transposable elements. Following this we will describe a mathematical model of molecular evolution, based on TE information that will allow for the identification of genes that have undergone a change in their strand-symmetry classification sometime over the last one-hundred million years. Note: This talk will assume an audience with a background in mathematics or the quantitative sciences. No knowledge of biology will be required, though some may be inflicted.

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