- How are PARS-assisted structure predictions generated and how are they displayed?
To generate the PARS-assisted structure predictions, we provide
the prediction algorithm (Vienna's RNAfold) constraints extracted
from our experimental measurement. Namely, nucleotides having a high
PARS score (>5) are constrained to be double-stranded whereas
nucleotides having low PARS scores (<-5) are constrained to be
single-stranded. Technically, this is done by using the constraints
options (-C flag) of RNAfold version 1.6. Those nucleotides that were used as
constraints are circled in the RNA structure plot shown at the browse
catalogs section and in iPARS.