They show a relatively high structural conservation (high structure conservation index, SCI) whereas the sequence similarity (expressed as main pairwise identity, MPI) is small.
An sci close to 1 indicates perfect structure conservation, while alignments without structural conservation yield values close to 0. A more detailed discussion of the sci can be found in [ 16] in the context of RNA alignment.
To test for the presence of conserved secondary structures, the SCI (structure conservation index) was calculated for each CNE alignment and used to compute the probability of a conserved secondary structure.
To study how protein structure conservation modulates sequence divergence, we recently developed the Structurally Constrained Protein Evolution (SCPE) model [ 14].
The estimation of sequence and structure conservation of selected protein regions is performed using constructed structural models and identified protein sequence and structure homologs.
Each candidate shows a highly conserved H box and ACA motif as well as high secondary structure conservation with two separate stem loop regions.
A structure conservation index (SCI), a measure of secondary structure conservation among input sequences, is derived from these two outputs.
Being fundamental functional RNA elements, many pre-miRNAs have maintained sequence and secondary structure conservation across large evolutionary distances.
In addition to sequence similarity, the nine sites had a high degree of structure conservation, with similar solvent-accessible surface and secondary structure (Table 3).
We analyzed the Drosophila retinoblastoma proteins to determine the extent of sequence and structure conservation of the N-terminal domain between flies and humans.
