< Back to Article

The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment

Figure 2

Near-identical Api-AP2 profiles from two parasites with very different background frequencies.

For P. falciparum (A, B) and T. gondii (C, D), the logos [120] (http://weblogo.berkeley.edu/) represent the letters aligned in the columns of the core Api-AP2 patterns (A, C). In the letter clouds (http://www.wordle.net/advanced) (B, D), the area occupied by each letter indicates the background frequency of an amino acid in the input sequence set (compare Fig. 2.1 of [49]). Colors represent various amino acid classes. For both organisms, Programs 1 or 2, run with Dirichlet mixture priors , or , converged on essentially the same 53- to 54-column core models that correspond to these logos. Api-AP2 models and logos almost identical to these were also obtained from other apicomplexan parasites Cryptosporidium hominis, Babesia bovis, Theilleria parva, and from the basal alveolate Perkinsus marinus, whereas the distantly related plant AP2 domains and HNH homing endonuclease/integrase domains gave distinct characteristic patterns similar in parts to Api-AP2 (data not shown). Thus, the core structural features of the Api-AP2 domain have been strongly conserved in long-diverged members of the Alveolata, following an ancestral gene expansion, whereas the background amino acid content of these organisms is strikingly different due to genome-wide drift.

doi: https://doi.org/10.1371/journal.pcbi.1000852.g002