Professor Jotun Hein " Comparative Virus Annotation "

Genome Annotation and Selectional Analysis of Viral Evolution

Genome Rearrangement in Mitochondria and Its Computational Biology

An evolutionary model for protein-coding regions with conserved RNA structure.

Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies exist, both between nucleotides occupying the same codon and between nucleotides forming a base pair in the RNA structure. The overlap of these fundamental dependencies is sufficient to cause "contagi...

Large-Scale Comparative Annotation of Bacterial Genomes

The MSc thesis describes the design and evaluation of a comparative annotation system for prokaryotic genomes. The proposed system makes use of a combination of comparative and abinitio gene finding techniques for accurate annotation. The three main modules described in the system are the markov-model based gene finding module, the alignment based profiler and the comparative module that combin...

Gibbs Sampler for Statistical Multiple Alignment

For a set of sequences, related by a binary tree, that have evolved according to the Thorne-Kishino-Felsenstein model, a Gibbs sampler is presented for simulating the ancestral sequences and their alignments. The updating step consists in updating the ancestral sequence and its three alignments within a 3-star tree. We compare the Gibbs sampler with the algorithm suggested recently by Holmes an...