Abstract

In contrast to the fairly reliable and complete annotation of protein-coding genes in the human genome, comprehensive information for non-coding RNAs is still lacking. Both quality and coverage of ncRNA annotation is not comparable to that of protein coding genes. In this presentation I will focus on the bioinformatics aspects of this “modern RNA world”. In particular, approaches towards annotating the plethora on ncRNAs and ncRNA candidates, and first studies into the evolution of these transcripts at genome wide scale will be discussed. RNA gene finding is a difficult task. While RNAs with evolutionary conserved secondary structure can be found by a combination of structure prediction and comparative genomics, little is known for unstructured RNAs. The conservation of transcript structures, however, provides a promising starting point. Complementary to gene finding, the recognition of members of known classes and the classification of novel transcripts posed important computational problems. We will briefly touch upon these topics in the context of microRNAs and snoRNAs, and discuss efficient structural clustering approaches.