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Table 1 Optimizing reference alignments of BRAliBase.

From: ConStruct: Improved construction of RNA consensus structures

  BRALIBASE CONSTRUCT
Alignment APSI SCI APSI SCI
   cov w/o cov   cov w/o cov
g2intron/aln51 0.46 0.55 0.42 0.45 0.75 0.58
rRNA/aln74 0.49 0.68 0.53 0.50 0.81 0.61
tRNA/aln27 0.35 1.19 0.73 0.36 1.22 0.76
U5-RNA/aln41 0.50 0.61 0.42 0.50 0.65 0.49
  1. For each RNA family used in BRALIBASE [7] we extracted the hardest alignment, i. e. the alignment with lowest sequence identity (measured as average pairwise sequence identity; APSI), and corrected it using CONSTRUCT. Quality measures for the original BRALIBASE alignments and the alignment optimized with CONSTRUCT are shown: sequence identity is measured as APSI, structural conservation as structure conservation index (SCI) with (cov) and without (w/o cov) covariation term, respectively. By using CONSTRUCT, the structural conservation of the alignments is clearly enhanced while maintaining sequence conservation. Dotplots of the alignments are shown in Table S1 of Additional file 1.