In partial fulfillment of the Requirements for the Degree of
Doctor of Philosophy

Catherine Putonti
will present her dissertation

Computational Methods for the Design of Ultraspecific Pathogen Signatures

Abstract
Designing nucleic acid-based assays for pathogen identification and detection with the necessary specificity, sensitivity, and reliability is computationally challenging. Using the set of novel algorithms and data structures introduced in this manuscript, it is now possible to efficiently calculate the frequency of all subsequences (n-mers) of length 5 to 25+ nucleotides in any sequenced genome. These algorithms can also compute all sequences one, two, three, etc. changes away from the nearest genome sequence. Thus, all subsequences present in or within a certain number of changes from the host/background genome can be excluded in the signature design step with greatly increased speed and predictability in comparison to current alignment-based methods. An evolutionary programming approach has been developed to complement these algorithms and data structures to identify the optimal combination of signatures. This new computational approach has lead to the creation of a new, more robust technology for pathogen identification

Date: Monday, April 17, 2006
Time: 3:30 PM
Place: 232 PGH

Faculty, students, and the general public are invited.
Advisor: Dr. Yuriy Fofanov