The first involves homology search, although these techniques are by definition unable to find new classes of ncRNAs.
The second category includes algorithms designed to discover specific types of ncRNAs that have similar properties.
Finally, some discovery methods are based on very general properties of RNA, and are thus able to discover entirely new kinds of ncRNAs.
Any algorithm that is designed for homology search of nucleic acid sequences can be used, e.g., BLAST.
Of particular importance for RNA is its conservation of a secondary structure, which can be modeled to achieve additional accuracy in searches.
[13] Mutations that change the nucleotide sequence, but preserve secondary structure are called covariation, and can provide evidence of conservation.