To optimize the resolution of the evolutionary relationships, alignment lengths were extended by including conserved motifs specific to each group of homologues (Figure 2, and Table S2).
The observation that 'deep' scoring matrices produce overextended alignments between domains that are less evolutionarily distant (have higher identity) than the scoring matrix target identity is not surprising, though the relationship between alignment boundaries (in contrast to internal alignment accuracy) and scoring matrices has not been extensively studied.
Impact equal to zero would imply that removing the layer from the network would not change the distribution of the WS values at all. Figure 7 (right) shows the relationship between Alignment and Impact across all the organizations.
In the present study, we identified the P-type II Ca2+ATPases from rice by analyzing their phylogenetic relationship, multiple alignment, cis-regulatory elements, protein domains, motifs and homology percentage.
Additionally, we provide qualitative evidence of this relationship through alignment comparisons.
To specify this relationship, an alignment of selected RAYTs together with reference set of "typical" IS 200/IS 605 transposases was constructed.
However, we find no relationship between alignment length and evolutionary distance in either of the core sets (11-way core set: Radj = 0.05, P = 0.25; 15-way core set: Radj = 0.03, P = 0.26).
The first observation made after analyzing the solution trajectory of the benchmarks was the imperfect relationship between Alignment Score, which is purely dependent on the Scoring matrix (BLOSUM62 in this case), and the BALiBASE score, which is purely based on biological facts.
Similarly, we can define the 'contained' relationship between alignments (a stronger condition) and between an alignment and a match.
These statistics are often used as thresholds to distinguish alignments likely to be due to a biological relationship from alignments that occur simply by chance.
