PSU Mark
Eberly College of Science Mathematics Department

Meeting Details

For more information about this meeting, contact Andrew Belmonte, Hope Shaffer.

Title:Topological pressure and a priori coding sequence density estimation in the human genome
Seminar:Seminar on Mathematics in the Bio and Geo Sciences
Speaker:Dan Thompson, Dept of Mathematics, Penn State
Abstract:
This is joint work with David Koslicki (Penn State). Inspired by concepts from ergodic theory, we introduce a new approach to coding sequence (CDS) density estimation for the human genome. Our approach is based on the introduction and study of topological pressure: a quantity assigned to any finite sequence based on an appropriate notion of `weighted information content'. For human DNA sequences, each codon is assigned a suitable weight, and using a window size of approximately 60,000bp, we obtain a very strong positive correlation between CDS density and topological pressure. The weights are selected by an optimization procedure, and can be interpreted as quantitative data on the relative importance of different codons for the density estimation of coding sequences. This gives new insight into codon usage bias which is an important subject where long standing questions remain open. We emphasize that topological pressure is a flexible tool and we expect it to be useful for the investigation of many other features of DNA sequences such as interspecies comparison of codon usage bias. We give a first result in this direction, investigating CDS density in the mouse genome and comparing our results with those for the human genome.

Room Reservation Information

Room Number:MB106
Date:11 / 16 / 2011
Time:01:00pm - 02:00pm