Fig. 1

Schematic representation of the workflow for the discovery of novel fungal ncRNA candidates. Noncoding IGRs and intron sequences were analyzed by BLAST to identify clusters of DNA sequences that are similar. The clusters were reduced in number by removing examples that are similar to known RNA motifs present in the Rfam database, and by searching for unannotated protein coding regions by using RNAcode [38]. The remaining clusters were examined by using CMfinder [28] to seek evidence for nucleotide sequence covariation and to develop preliminary secondary structure models. Pre-candidate RNA motifs (P1 designates pairing element 1; arrow identifies covariation site) with only a few covariations and few representatives were discarded. Finally, Infernal was used to search for additional representatives that might have been missed in the initial search, and to refine the consensus sequence and secondary structure model. The refined candidate ncRNA depicted is the novel motif rpl7 reported in this study