We have confirmed that the resulting post-fabrication type-I collagen structure retains the essential phase behaviour, alignment and spectral characteristics of aligned native type-I collagen.
According to the Dayhoff model, orthologous sequences evolving in two different lineages will asymptotically approach the saturation percent identity value characteristic of alignments of unrelated sequences (formula 1).
Alternatively, if the automatic selection of parameters options is selected, trimAl will compute specific score thresholds depending on the inherent characteristics of each alignment.
It wraps a conservative shuffling procedure that maintains local characteristics of an alignment, e.g. columns with the same gap and conservation pattern.
Our observations on alignment and topological comparison measures are important for future multiple analysis studies as far as they indicate that the shape of the tree cannot always be predicted from the descriptive characteristics of the alignment, at least in the case where highly divergent sequences are considered.
In the mechanical transmission field, shaft hub couplings with polygonal profiles play an interesting role because of their characteristics of self-alignment, lack of projecting elements (responsible for high stress concentration) and constructive compactness.
Random sequences can dilute the position-specific amino acid exchange characteristics of native alignments.
This database encompasses characteristics representative of alignments manually annotated, including members of a particular enzyme family, according to the Enzyme DB [ 71].
Since reviews about characteristics and properties of alignment methods have been published elsewhere [ 26, 67, 78], we do not report a comprehensive list but rather a shorter list of 17 commonly used tools and refer to the literature for an in-depth review of the methods and the corresponding tools.
