In general, note that relaxing parameters does not necessarily increase coverage because this can lead to an increase in the number of conflicting candidate pairs as well, and those are excluded from predictions by ESPRIT (see Methods section).
We set the penalty parameters β 1=35, β 2=20, for the ATV case, β 1=100, β 2=20 for the ITV case and relax parameter γ=1.618.
The pipeline runs alignments with both default and relaxed parameters.
These relaxed parameters introduced more noise into the results, and likely increased false positives.
In order to enlarge the list of enriched transcripts in Hcrt neurons, relaxed parameters were set and the new requirements were 10 TPM and 3.6 times higher abundance in EGFP+ cells compared with the control groups.
Instead of using automatic annotations, we searched for each C/D snoRNA in the vertebrate genomes using the WU BLAST 2.0 algorithm with specifically selected relaxed parameters; and the results of each search were manually inspected [ 16].
For example, if experimental evidence suggests that an mRNA is regulated by miRNAs, yet it is not among the group predicted using the stringent screening parameters, then relaxing different parameters one by one would produce a set of candidate miRNA regulators.
The threshold was chosen after testing different cutoff values: relaxing this parameter did not produce substantial changes in the number of shared CDSs, while tightening the percentage identity cutoff resulted in a rapid decrease in the number of shared CDSs (see Additional file 1: Figure S1).
A practical approach is advocated, in which the most important dimensionless parameters are matched to a reactor in the reduced-size device, while relaxing those parameters which are far from a threshold in behavior.
