Bioinformatics Preprint 05-023
Prediction of Structured Non-Coding RNAs in the Genomes
of the Nematodes Caenorhabditis elegans and Caenorhabditis briggsae
Kristin Missal, Xiaopeng Zhu, Dominic Rose, Wei Deng, Geir Skogerbø, Runsheng Chen, Peter F. Stadler
We present a survey for non-coding RNAs and other structured RNA motifs in the genomes of C.elegans and C.briggsae using the RNAz program. This approach explicitly evaluates comparative sequence information to detect stabilizing selection acting on RNA secondary structure. We detect 3672 structured RNA motifs, of which only 678 are known ncRNAs or clear homologs of known C.elegans ncRNAs. Most of these signals are located in introns or at a distance from known protein-coding genes. With an estimated false positive rate of about 50% and a sensitivity on the order of 50% we estimate that the nematode genomes contain between 3000 and 4000 RNAs with evolutionary conserved secondary structures. Only a small fraction of these belongs to the known RNA classes, including tRNAs, snoRNAs, snRNAs, or microRNAs. A relatively small class of ncRNA candidates is associated with previously observed RNA-specific upstream elements.
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