Reliable structural genome annotation of Archaea

• Applicant: Privatdozentin Dr. Katharina Hoff
• Subject Area: Bioinformatics and Theoretical Biology
• Term: from 2010 to 2014
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 185374917

Archaea are organisms that have adapted to extreme habitats. For instance, they tolerate high temperatures, high salt content or low pH. They are interesting candidates for basic research and industrial applications. Therefore, numerous archaeal genomes have already been sequenced.Up to now, the annotation of archaeal genomes was pursued mostly by using statistical models that were developed for predicting genes in Bacteria. In contrast to Bacteria, Archaea share many elements of transcription and translation with Eukarya. A major aim of the proposed project is to find out whether archaeal gene structure annotation can be improved by integrating models that take archaeal genome properties into account.State of the art gene finders for eukaryotes already integrate experimental evidence like proteome and transcriptome data. Such data is also produced for Archaea. In order to improve annotation quality of archaeal genomes, I propose the development of a gene finder that includes special features of Archaea (e.g. a model for archaeal promotors) and integrates experimental evidence.The new tool will be available to the research community as a command line tool and as a web server application. All genome annotation data generated through this project will be made available in GenBank format, and in a format for visualization with the USCS Archaea Browser.Features of archaeal and bacterial genes (including UTRs and some range of up- and downstream regions) will be compared on a large scale in order to detect principle differences between archaeal and bacterial genes. For instance, previous publications in the field lead to the expectation of significantly different translation initiation site features. Aim of this proposal is to find out whether such differences are universal archaea/bacteria differences, or whether they are characteristic for some few species.

• DFG Programme: Research Grants