Computer Science Colloquium
Pathogens Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
Rules, rather than genesMon 28.08.2006, 11:00, 60 minutes
AbstractDespite the many genomic sequences and gene annotations available, how genetic information is structured in any genome remains poorly understood. Eukaryotic parasites subtelomeres provide a unique system to tackle this question, as they are crucial effectors of adjacent contingency genes (including virulence genes) in these organisms, and as subtelomeric-sequence assemblies are available for most of them. Yet their intrinsic features have undermined so far a comprehensive analysis. An intuitive approach will be outlined, based on the integration of dot-plot analyses, of softwares publicly available and of Perl scripts developed locally. Its application demonstrates how in-depth large-scale annotation of junk DNA may help understanding the mechanisms underlying plasticity and mosaicism at the chromosomal ends, the mechanisms of allelic exclusion and antigenic variation observed among virulence-related genes, and foster convergence between experimental, evolutionary and in silico studies. Lastly, to begin to uncover the implicit information of a genome, an empirical, linguistically informed approach was undertaken to describe and compare subtelomere architecture in lower eukaryotes. Although the design features of these domains are admittedly diverse, variation is restrained. This suggests the existence of universals of chromosome architecture similar to the universals of language proposed by Chomsky, and points to the possibility of using organism-neutral syntax and vocabularies to uncover principles of genome architecture.
Invited by Prof. Sepp Hochreiter
The Computer Science Colloquium is organized by the Department of Coputer Science at JKU, the Österreichische Gesellschaft für Informatik (ÖGI) and the Österreichische Computergesellschaft (OCG).