Scores
Just as in the previous BRAliBase II benchmark [22] we used the SCI [44] to score the structural conservation in alignments. The SCI is defined as the quotient of the consensus minimum free energy plus a covariance-like term (calculated by RNAALIFOLD; see [45]) to the mean minimum free energy of each individual sequence in the alignment. A SCI ≈ 0 indicates that RNAALIFOLD does not find a consensus structure, whereas a set of perfectly conserved structures has SCI = 1; a SCI ≥ 1 indicates a perfectly conserved secondary structure, which is, in addition, supported by compensatory and/or consistent mutations. The SCI can, for example, be computed by means of RNAZ [44]. To speed up the SCI calculation we implemented a program, SCIF, which is based upon RNAZ but computes only the SCI. SCIF was linked against RNAlib version 1.5 [46,47].
In [22] we used the BALISCORE, which computes the fraction of identities between a trusted reference alignment and a test alignment, where identity is defined as the averaged sequence identity over all aligned pairs of sequences. Because the original BALISCORE program has certain limitations and peculiarities, e. g. skips all alignment columns with more than 20 % gaps, we instead used a modified version of COMPALIGN [43] called COMPALIGNP, which also calculates the fractional sequence-identity between a trusted alignment and a test alignment. Curve progressions for scores computed by BALISCORE and COMPALIGNP are only marginally shifted. The COMPALIGNP score is called SPS' throughout the manuscript.
As both scores complement each other and are correlated, we use the product of both throughout this work and term this new score BRALISCORE.