Section: Application Domains
Our expertise in sequence analysis also applies to noncoding RNA. Noncoding RNA plays a key role in many cellular processes. First examples were given by microRNAs (miRNAs) that were initially found to regulate development in C. elegans, or small nucleolar RNAs (snoRNAs) that guide chemical modifications of other RNAs in mammals. Hundreds of miRNAs are estimated to be present in the human genome, and computational analysis suggests that more than 20% of human genes are regulated by miRNAs. To go further in this direction, the 2007 ENCODE Pilot Project provides convincing evidence that the Human genome is pervasively transcribed, and that a large part of this transcriptional output does not appear to encode proteins. All those observations open a universe of “RNA dark matter” that must be explored. From a combinatorial point of view, noncoding RNAs are complex objects. They are single stranded nucleic acid sequences that can fold forming long-range base pairings. This implies that RNA structures are usually modelled by complex combinatorial objects, such as ordered labeled trees, graphs or arc-annotated sequences.