Analysis of the adjacent nucleotide or base pair dependency of known ncRNAs and other candidates reported by Infernal.

The second and the third columns show the number of known members and other candidates reported by Infernal for some families. The column 4,5,6 (or 7,8,9) show the comparison of the dependence of adjacent nucleotides along single-stranded regions (or adjacent base pairs along stacking pair regions) between all known ncRNA members (i.e. full members) in Rfam and the other candidates reported by Infernal of each family. Larger value of (or ) indicates the higher level of dependence between the adjacent single-stranded columns (or paired columns) within the multiple sequence alignment . The table lists the top 20 families with the highest number of candidates reported by Infernal. As we can see, in most of the cases, the level of adjacent dependence along both single-stranded regions and stacking pair regions in known ncRNAs is higher than that in other candidates reported by Infernal. The % of difference between the dependence levels with respect to the values of other candidates are 164% and 109% along single-stranded regions and stacking pair regions respectively. This provides evidence to support our conjecture that the adjacent dependence in human ncRNA molecules should be useful to distinguish real ncRNAs from false positives.