The phrase "a given alignment of" is correct and usable in written English.
It can be used when discussing a specific arrangement or configuration of elements in a particular context, such as in mathematics, biology, or data analysis.
Example: "In this study, we will analyze the effects of a given alignment of genes on the overall health of the organism."
Alternatives: "a specific arrangement of" or "a particular configuration of".
Then one run of the method involves only summing corresponding pre-calculated values for all 20 amino acids, and for a given alignment of ~100 sequences of length ~400 aa it takes approximately 50 ms (AMD Athlon™ 64 Processor 3800+).
To this end, we used PhyloCSF, which reports a log-likelihood ratio reflecting the relative probabilities of observing a given alignment of orthologous nucleotide sequences under models of protein-coding or non-coding evolution (Lin et al., 2011).
Specifically, we consider a given alignment to consist of discrete segments of constant sample size, with observed segregating sites estimated based on the Bayesian posterior probability of a SNP at each position calculated by GigaBayes as described above.
To analyze a given alignment A of extant sequences, we first determine the probability of the alignment under the maximum likelihood estimate (MLE) of the parameters for the coding model, p C =maxθ C Pr(A|Coding,θ C ).
However, the group was not sensitive to phylogenetic model selection as both MrBayes and phyML generated consistent topologies for a given alignment irrespective of the substitution model.
The score of a given alignment is the sum of correlations between corresponding segments.
For a given alignment, the entropy of an amino acid position H x) is defined as H x) = −∑ P x) log P x) where x is one of 20 amino acid residue types.
Thus, for a given alignment, the corresponding shortened alignment of length 10 is contained in the shortened alignment of length 25, which is contained in the shortened alignment of length 50, and so on.
For example, when we estimate the functional score of a given alignment, there is rarely >15 20% of pairs with GO annotations.
In a general way it must be understood that a given alignment is the result of a compromise between contradictory requirements: for example, minimum gradient and minimum earthworks; minimum earthworks and length of route.
These methods typically aim to maximize a function that describes the fit of a given alignment or tree instance to the data, using a model of sequence substitution to represent rates of evolutionary change between different types of nucleotide or amino acid residue.
