Annotation of genomes is an important process which increases the usefulness of genomic data immensely. However, there are many annotation tools in use, and they can all give different results. This master project is about creating a framework for comparing annotations from various sources. This is done in the context of annotation of ribosomal RNAs, or rRNA, in genomes. Knowledge of the rRNA and its location in a genome is very useful for working out evolutionary relationships among organisms. This because they are of ancient origin and are found in all known forms of life. So there is a lot to gain by finding them. The program being made gives the possibility to compare and analyze the available as well as future predictor programs. This is useful for making a choice of which to make use of and a helpful tool for continued development of these programs.