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In order to calculate constraint scores for Agrp exons, the STAT sites, and the IREs, we modified the concept of an RS score, such that the score for constraint represents the sum of constrained alignment columns in these regions while ignoring unconstrained alignment columns.
We used nucleotides from the fastest evolving intronic (FEI) sites as putatively neutral standards to calculate constraint.
It is important to emphasize that all the test cases considered in this work, and in previous works, do not employ in anyway the DCM to calculate constraint probabilities.
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Eco-physiological modelling of forest production relies heavily on local meteorological data in order to calculate constraints of photosynthesis, and we need to clearly identify the precision and bias associated with sources of such data.
Other impediments given were time to implement, long paybacks, or paybacks that were too difficult to calculate, constraints on buildings, such as being in a leased or listed building, or being only in a short-hold tenancy from which the occupants may not gain any benefit from installing new equipment such as solar panels.
We calculated constraint by comparing E to numbers of observed substitutions (O): C = 1 - O / E Standard errors and confidence limits for C were calculated by bootstrapping the data values of O and E 1000 times.
For all repetitions, we calculated constraints at paired and unpaired sites in the large and small sets, respectively, and thus obtained distributions for | CA − Cx| that would be expected at random (fig. 4).
Use the opportunistic calculation method to determine whether the set meets the opportunistic to calculate the constraint conditions.
In order to calculate the constraint distance between the landmark and target, we also need to compute the conversion relationship between the delay and the distance, after getting the estimated delay and possible areas of the landmark.
To confirm our results from sliding window analysis we used a software package called SWAPSC, which similarly uses a sliding window analysis procedure to calculate selective constraint [54].
This amounts to calculate a constraint alignment by LocARNA, which restricts the search space and thus speeds up LocARNA.
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