It relies on the subroutines Align, which returns the best alignment between two series based on a given set of genes, and ScoreGene, which returns the score of two series when aligned using a given alignment and a specified gene.
GENECONV is a computational program for statistically detecting high-scoring aligned pairs in a given alignment [ 28].
In this context, it can further be stated that "saturation" is not an inherent character of an aligned sequence position in a given alignment, it rather depends on the considered phylogenetic level.
Moreover, Golubchik et al. ([3]) showed that the absence of amino acid residues often leads to an incorrect placement of gaps in the alignments, even when the sequences were otherwise identical, and, for a given alignment, not all amino acid positions will be aligned with equal confidence [4].
Based on that given cross-sectional parameters as well as based on a given alignment, a 3D model can be parametrically derived.
The lengths of alignments were also trimmed so all sequences in a given alignment were the same length.
For a given alignment identity x, let Ix be the set of target strains with which the first segment has identity at least x.
This could probably be because our program does not discriminate between the nature of amino acid present in DHA1 and SP families at a given alignment position.
When all models generated for a given alignment have been evaluated, the predictor score distribution of the formers is assigned to the latter.
The randomization was achieved by shuffling residues across sequences at a given alignment position as done by Mirny and Genfand [51].
Once the maximum likelihood for all available models is estimated and merged into a file by PalmDaemon, statistical information of the parameters can be accessed to evaluate the fitness of a model for a given alignment.
