The higher the score is for a pairwise alignment, the higher the degree of conservation is between the two aligned sequences.
Structural-diffusion data alignment: The high-resolution 3DT1w volume was realigned to the diffusion data by inverting the full-affine transformation (12 degrees of freedom, FLIRT, FSL) (Jenkinson et al. 2002 ) from diffusion to high-resolution space.
This alignment shows the high degree of sequence conservation between cyanobacterial H-NOB sequences and the sequences in the basal animal sGC clade.
Synonymous and non-synonymous substitution rates were calculated by the Synonymous/non-synonymous Analysis Program (SNAP) provided by Los Alamos National Laboratory using the codon-based NA alignment of the high homology group.
Single-best mappings were derived from IndexDP alignments by choosing alignments with the highest NScore, or an alignment randomly picked from the set of highest scores when multiple alignments are present with the same NScore value.
Although the 2-10° range for anatomic limb alignment showed the highest accuracy, anatomic alignment was not accurate in most knees with any of the three methods (3 9°, 65 %; 5 10°, 67%%; 2 10°, 73 %) (Table 2).
Early chromosomal alignments demonstrated the high level of recombinations and rearrangements in Thermococcales genomes [6].
Orthologous and paralogous protein alignments, showing the high conservation of each amino-acid altered by missense mutations in vertebrates and in the delta protocadherin paralogous genes.
Several examples of multiple sequence alignments depicting the high conservation of these RUFs among different trypanosomatid species are shown in Figure 4.
