CeBiTec Colloquium: Dr. Matthias Höchsmann, University of California, Santa Cruz

2007/12/17 5:15 p.m.
CeBiTec Laboratory Building, Room G2-104

The UCSC Archaeal and Extremophile Genome Browser

As more archaeal and bacterial genomes are sequenced, effective research and analysis tools are needed to integrate the diverse information available for any given locus. The feature-rich UCSC Genome Browser, created originally to annotate the human genome, has become one of the most appreciated research tools for studying eukaryotic genomes. The UCSC Archaeal Genome Browser provides this framework for currently 50 archaeal and selected bacterial genomes. Among the core annotation tracks are G/C content, gene and operon annotation from multiple sources, sequence motifs (promoters and Shine-Dalgarno), microarray data, multi-genome alignments and protein conservation across phylogenetic and habitat categories.
In this talk I give a summary of the UCSC Archaeal Genome Browser and archaea research. I also demonstrate that not only biological but also bioinformatic studies do benefit from a framework where diverse information is gathered and can be analyzed computationally and visually. Traditionally, visual genome exploration is limited to sequential data and predominantly considers features of protein coding genes. Among other useful RNA tracks, I will present a visualization of the RNA secondary structure space for any given locus in a genome.