Hidden Markov models for the prediction of transmembrane protein localization in eukaryotes
Speaker: Stefan Maetschke, ITEE
When: 2005-07-20 10:30:00
Venue: 78-622
Host: Marcus Gallagher
Abstract:The widening gap between the growing number of protein sequences and
the understanding of their function demands the application of
computational analysis, since in vivo and in vitro experiments
cannot keep pace with the explosion of biological data. One
important physical aspect in eludicating the function and
interaction of proteins is their subcellular localization.
Recent years have seen the development of many prediction algorithms
for subcellular localization. Most of them focus on prokaryotic or
soluble proteins and achieve only low accuracies when applied to the
localization of eukaryotic transmembrane proteins. Transmembrane
proteins however, are of special interest since they are difficult
to crystallize and therefore hard to study, but on the other hand
essential for the composition and function of the compartment
membranes.
Within this research project a novel, hidden Markov model based,
prediction method will be developed to address three questions:
First, are hidden Markov models superior to current methods for
predicting the subcellular localization of eukaryotic transmembrane
proteins. Second, which signals control the localization of
transmembrane proteins in eukaryotes and third, how can highly
variable patterns in sequential data, such as localization signals,
be described with hidden Markov models.
The performance of the new prediction algorithm will be evaluated on
two datasets. The first one is a subset of the mouse proteome,
containing transmembrane proteins with experimentally confirmed
subcellular localizations. The second one is a selection of
eukaryotic transmembrane proteins from the Swiss-Prot database.
Biography:(biography unavailable)
Type: Ph.D confirmation
Contact:Marcus Gallagher, seminar host (marcusg@itee.uq.edu.au)
or Guido Governatori (ITEE seminar co-ordinator)
(guido@itee.uq.edu.au)