Flowchart of the computational methods used by Breaker et al.  in the identification of candidate ncRNA motifs. The steps in the process were as follows: (a) Identify IGRs by size, %GC content; (b) eliminate ncRNA motifs of known structure, such as tRNAs, rRNAs and annotated riboswitches; (c) find conserved IGR sequences in other genomes using BLAST analysis of the CAMERA database, and exclude protein-coding regions; (d) align IGRs and predict conserved secondary structures using CMFinder; and (e) search for homologs using conserved secondary structure criteria. Green indicates a candidate ncRNA motif.
Hwang et al. Journal of Biology 2009 8:72 doi:10.1186/jbiol174