Visualizing Orthologs, turn-over, and remolding of tRNAs
Type of thesis: Masterarbeit / location: Leipzig / Status of thesis: Finished theses
Transfer RNAs (tRNAs) are ubiquitous in all living organism. They implement the genetic code so that most genomes contain distinct tRNAs for almost all 61 codons. They behave similar to mobile elements and proliferate in genomes spawning both local and non-local copies. Most tRNA families are therefore typically present as multicopy genes. The members of the individual tRNA families evolve under concerted or rapid birth-death evolution, so that paralogous copies maintain almost identical sequences over long evolutionary time-scales. To a good approximation these are functionally equivalent. Individual tRNA copies thus are evolutionary unstable and easily turn into pseudogenes and disappear. This leads to a rapid turnover of tRNAs and often large differences in the tRNA complements of closely related species. Since tRNA paralogs are not distinguished by sequence, common methods cannot not be used to establish orthology between tRNA genes.
In this Master Thesis we will visualize the results of an existing pipeline for detecting tRNA orthologs. Besides various visualizations for the results we will revise the output files and the pipeline design. At the end of this work we will prepare the pipeline and the visualizations for deploying a public available service for detecting orthologs in gene families like tRNAs.