This amounts to calculate a constraint alignment by LocARNA, which restricts the search space and thus speeds up LocARNA.
The definition of possible gene regions, gene annotation, and PCG codon position were determined against published references of Euploea mulciber, Argynnis hyperbius, Athyma sulpitia, Kallima inachus, and Hipparchia autonoe (Additional file 1) by using Sequencher and alignment by eye which was straightforward at codon level.
The absolute value of the likelihood, normalized for sequence length, is used as the metric by which alignment robustness is measured.
During core building, a smoothed fragment-based environment-specific substitution score Scand is used to determine the order, by which alignment columns are added to the model's core.
1) The rationale underlying the analysis approaches should be explained more clearly: In the Introduction: "We hypothesized that RATN theta phase alignment may provide the mechanism by which RATN synaptic modification required for memory formation occurs…".
The probability by which each alignment column is produced by the different genealogies in the model is readily computed by posterior decoding of the fitted HMM. Figure 2B shows the probability of each genealogy along 3kb of a genomic alignment of chromosome 2 from human, chimpanzee, and gorilla.
However, several substantive concerns were expressed by the reviewers: 1) The rationale underlying the analysis approaches should be explained more clearly: In the Introduction: "We hypothesized that RATN theta phase alignment may provide the mechanism by which RATN synaptic modification required for memory formation occurs…".
The reference-dependent alignment accuracy is calculated as the percentage of correctly aligned positions judged by reference alignments, which are generated by structural alignment programs.
Based on the insight of the pros and cons of these two approaches, we present a new alignment algorithm, Ontology Alignment by Artificial Neural Network (OAANN), which combines rule-based and learning-based solutions.
The investigator must specify the parameters of all ϕ = (ϕ 1, 1, …, ϕ Y, k Y ) substitution models by which the alignments evolved along the G = (G 1, 1, …, G Y, k Y ) gene trees.
