Bioinformatics methods for comparative genomics

A list of exjobb projects:
The projects typically involve either analyzing existing or new methods, or design user-friendly interfaces to them. Most projects will be in the area of comparative genomics, phylogenetics, or functional genomics.

Some projects are:

- Develop a Java or HTML browser for integrating multiple protein structure/function preditions.

- Train a Support Vector Machine (SVM) model to discriminate efficient antisense oligos that can be used for functional genomics.

- Develop a browser for flexible visualization of gene locations on multichromosomal genomes.

- Comparative analysis of the accuracy of several tree-building methods.

- Analysis of the evolution of protein domain architectures.
For instance, how often have different evolutionary paths lead to identical domain arrangements? What are the functional similarities between such proteins?

- Analysis of the intron evolution over large timespans: To what extent are they retained, gained or lost? Is the intron evolution correlated with functional divergence?