These tRNAs have cloverleaf secondary structures that were derived by comparative analysis using an alignment that is most compatible with tRNA phylogenies and known 3-dimensional models of structure [91], [92].
Indeed there are many homologous proteins in different superfamilies and folds, e.g. many proteins in a/b class (Rossmann-like folds) are most likely homologous regardless of the fold they are placed into, and their detection by sequence search software with an alignment that matches structure-based alignment should not be counted as "false positive".
As a consequence, all alignments require inspection and interpretation, and often adjustment by hand, in order to produce an alignment that best represents the biological context of the sequences.
The best tree was selected by the alignment that produced the tree with the highest bootstrap values.
The alignment of orthologous coding sequences was guided by a multi-protein sequence alignment that was generated by MAFFT 6.849 [ 64].
The process of alignment requires the best overall match between the two sequences to be found first: this 'global alignment' is then followed by a finer-grained 'local alignment' that involves modifying the short sequences by, for example, inserting small gaps or deleting short stretches of the sequence.
Alternatively, we can guarantee convergence by using an alignment algorithm that is exact.
Additionally, each optical element is set by the alignment that a laser beam changes 10 nm on QPD, when a normal vector changes 0.1 μrad.
Briefly, sensitivity measures the fraction of the structural alignment that is correctly recovered by a given sequence alignment, while precision measures the fraction of a sequence alignment that correctly reproduces the structural alignment.
The perspectives show pleasant-looking open spaces, miraculously sunlit in what are canyons between the blocks, presumably made possible by the sort of occasional solar alignment that causes Stonehenge to light up at the summer solstice.
