The phrase "alignment of sites" is correct and usable in written English.
It can be used in contexts where you are discussing the coordination or arrangement of different locations or web pages, often in relation to design, strategy, or data.
Example: "The alignment of sites is crucial for ensuring a seamless user experience across our digital platforms."
Alternatives: "coordination of locations" or "arrangement of sites".
Decomposed alignment of sites identified by GUIDANCE as being well-aligned between and within SerRS and ThrRS paralogs (see methods).
The interactions between the protein ligand and the alignment of sites belonging to a cluster with the reference are displayed using a Jmol applet (http://jmol.sourceforge.net/).net/
Alignment was done with the RNA SALSA software [ 30], which aligns ribosomal RNA sequences by utilising existing hypotheses of structural patterns, in order to constrain thermodynamic folding algorithms and favour the alignment of sites that contain compensatory substitutions.
In conclusion, the PLIC database provides clusters of binding sites along with information about similarity among members within a cluster, common interactions in the cluster through alignments of sites, protein ligand contacts, binding site environment properties and binding energetics that help in analyzing various attributes of protein ligand interactions.
Note that in alignments of sites in a single genome we can observe only the equilibrium constants π n, π c (which actually are rather rough approximations), thus the assumption p nc = p cn may be too strong, and the above general formula for f cn might be more relevant.
We found 1,208 gene families present in all CTG taxa; these were concatenated together to give a nucleotide alignment of 1,291,068 sites or 860,712 sites when third codon positions are removed.
For every alignment, 20% of sites were set to be invariant.
We forbid the alignments of site segments of length below 6, e.g. any matched site has at least four other consecutive sites also matched.
GENECONV detects the evidence of recombination by assessing the significance of long tracts of identical sites among pairs of sequences in a multiple alignment of informative sites.
Nucleotide sequences from the resulting 19 strains were aligned using clustalw [ 35] into an alignment of 8555 sites that is subsequently used for phylogeny estimation with iqpnni [ 36].
In the case where 2 models have the same number of free parameters, 0.3 AIC per site is equivalent to ~45 log likelihood points per alignment of 300 sites.
