The amino acid substitution and composition in P. falciparum proteins were unusual and standard matrices (BLOSUM & PAM) did not detect orthologs and/or gave poor alignment for many P. falciparum proteins [ 9- 11].
The chapter presents nucleotide substitutions and composition in coding sequences.
The catalytic activity of the Mn-substituted barium hexaaluminates increases with Mn substitution, the optimum composition being obtained when about 3 Mn ions per unit cell are incorporated, as regards the activity and the resistance to ageing at 1200°C in the presence of steam.
The nucleotide composition, substitution rates, transition-transversions ratios and models of nucleotide substitution for alternative partitions of the data are summarized in Table 2. Homogeneity tests showed similar phylogenetic signals for each major data partition, although the two nuclear genes did exhibit marginally non-significant heterogeneity (ILD test, P = 0.056).
This file was imported into a Microsoft Excel spreadsheet and computations of the number of each type of nucleotide substitution and the composition of the flanking sequences around these substitutions were performed using macros in Excel (Visual Basic).
Values for the substitution matrix, base composition, gamma distribution of among-site rate variation (G) and the proportion of invariant sites (I) are available from the authors on request.
A maximum likelihood tree was constructed using the general time reversible plus gamma (GTR+G) model of evolution and bootstrapped with 100 replicates (parameters for nucleotide composition, substitution rates and gamma shape were estimated by PAUP) (see Additional file 5).
Specifically, the author tested substitutions at four-fold degenerate sites for the existence of a correlation between neighbouring base composition and substitution bias and found that substitution bias, as measured by the proportion of transversions, is significantly different when neighbouring bases differ in their A+T contents.
Since saturation of substitutions and base composition may violate reliability of results of phylogenetic analyses (especially based on nucleotide sequences) we carried out the appropriate tests to check it (see Material and Methods for details).
This might be due to the simplicity of our genome evolution model, which does not include other mutational processes, such as insertion and deletions that might have been acting against the influence of substitutions on base composition around and within genes.
