The overall likelihood is then the product of site likelihoods or the sum of site log likelihoods.
The context score is the sum of site-type contribution, 3' pairing contribution, local AU contribution, and position contribution.
The prediction efficacy is calculated as context +score of the sites which is the sum of site-type contribution, 3′ pairing contribution, local AU contribution and position contribution.
L input is the sum of sizes of these sites found in various proteins and L query is the sum of sizes of these proteins that contain these sites.
The total variability, σ total 2, was calculated as: σ total 2 = σ tissue 2 + σ RNA assay 2 where σ tissue 2 was estimated as the sum of the site-to-site and section component estimated in the tissue reproducibility study, and σ RNA assay 2 was estimated as the total variation from the RNA precision study.
The advantage of performing a locus-level analysis is that we expect f locus > f site because f locus is proportional to the sum of f site over all sites under selection in the locus.
Interestingly the strengths of the Met4 sites are not mainly determined by the strength of Met31 or Cbf1, but by the sum of these sites.
We calculated the sum of four sites (triceps, biceps, subscapular, and suprailiacal).
In the latter approach, the program needs to do the mass sum multiple times, repeating the mass sum of unvaried sites, and thus may slow down the searches.
Remarkably, the difference between the conformation of DBS (solid lines) and the sum of individual sites BS1 and BS2 (dashed lines) varies among the three E2C domains.
