Given a consistent reference alignment, selecting a reference sequence closely resembling the candidate sequence and transferring the alignment positions of the shared segments suffices to perfectly align those shared segments.
In contrast to the individual gene phylogenies, phylogenetic trees based on a concatenated alignment of 13 of the shared single copy genes show improved resolution and are similar to recently reported phylogenies [ 61, 62, 80, 81] though there are significant differences with the placement of individual species between the MP and ML trees.
Using the alignment partners of all housekeeping genes in the yeast interactome, we construct an alignment consistency table of size 1,540×79, which summarizes the network alignments over the shared subsection of tissue-specific networks.
We generated a concatenated alignment of these shared segments according to the gene order found in the CFN42 genome, and then inferred a consensus sequence and computed the number of nucleotide differences across windows of 250 bp.
The counts of the shared alignments were normalized to the total number of alignments for each map and used as similarity vectors in a hierarchical clustering analysis with the Spearman rank correlation as similarity measure (Fig. 4).
Interestingly, when we added the structure of the redesigned PPI (2erh) to our alignment, the shared pattern of interactions, detailed in Figure 2B remained almost unchanged.
Where, a training set representing the most active lead analogs [12, 13] was selected, energy minimized and submitted to flexible alignment for analyzing the shared spatial arrangement of their pharmacophoric features.
While the previous sets included mainly alignments of shared, structured domains, the reference set described here focuses on (i) subfamily specific features, (ii) motifs in disordered regions, (iii) the effect of fragmentary or otherwise erroneous sequences on MSA quality.
These alignments were used to construct a similarity matrix where each cell corresponded to the count of the alignments shared by each pair of metabolic maps.
The driving force was the alignment of shared interests around the commitment to train and deploy the 3000 midwives.
