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The aim of the study is the research of the alignment methods applied for the rotating kilns, their merits and disadvantages.
The robustness of the alignment algorithm applied to the elbow joint was completely characterized.
Bootstrap analysis with 1000 times replicates (Felsenstein, 1985) of the alignment was applied to maximun parsimony method.
Finally, to evaluate whether the 'sieving' method was able to identify residues of functional relevance for "difficult" alignments, it was applied to two FAD binding domains, d1gt8a4 and d1mo9a1 (Case (D), SCOP folds c.4.1.1.1 and c.3.1.5 respectively).
Subsequently, the PR is responsible for sensing the alignment direction and applying the appropriate filter.
Three measures were computed: (i) alignment conservation annotation measures the number of conserved physicochemical properties for each column of the alignment applying the approach used in the AMAS method [ 27]; (ii) alignment quality annotation is a measure of the likelihood of observing mutations (if any) in a particular column of the alignment.
In the areas between the pivotal alignments, the global alignment algorithm is applied.
Two strategies were implemented to align these orthologous sequences using the global alignment algorithm – mlagan: 1) optimizing the alignment parameters and 2) applying a post-alignment filter.
Finally, adjustments were made manually where this obviously improved the initial automated alignment (this applied to the majority of proteins analysed).
To isolate the effect of alignment we applied a linear SVM to the alignment model determined by the HMM.
Beginning with these sections, fiducial traces were placed on cross-sectioned microtubules or mitochondria in the same location, and the linear alignment feature was applied to bring the images into alignment.
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