Seminars at the Faculty of Informatics

Motif matching in DNA sequences using generalized PWM models

The Faculty of Informatics is pleased to announce a seminar given by Emanuele Giaquinta

DATE: Monday, April 13th 2015
PLACE: USI Lugano Campus, room SI-008, Informatics building (Via G. Buffi 13)
TIME: 13.30

The weighted matching problem consists in finding - given a weighted pattern P of length m and a string T - all the substrings of T of length m whose score with respect to P is larger than a given threshold. A classical application of this problem in computational biology is to find transcription factor binding sites in DNA sequences, using a motif model known as Position Weight Matrix. In this talk I shall present algorithms to solve the weighted matching problem using generalized versions of the Position Weight Matrix model, which allow for more accuracy.

Emanuele Giaquinta is a postdoctoral researcher at Aalto University, Espoo, Finland. He received a M.Sc. and a Ph.D. degree in Computer Science from the University of Catania, Italy, in 2007 and 2011, respectively. From 2012 to 2014 he held a postdoctoral position at the University of Helsinki, Finland. His research interests include string algorithms, combinatorial algorithms, and computational biology.

HOST: Prof. Laura Pozzi