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Figure 1 | BMC Bioinformatics

Figure 1

From: The ancient history of the structure of ribonuclease P and the early origins of Archaea

Figure 1

General methodological approach. The flow diagram in the left describes the phylogenetic reconstruction of trees of molecules and substructures. The structure of RPR molecules can be deconstructed into substructures, such as coaxial stem tracts and unpaired regions, that can be studied using features (characters) that describe their geometry and shape (e.g., length of stems or unpaired regions). These structural characters are coded and assigned "character states" according to an evolutionary model that polarizes character transformation towards an increase in molecular order (character argumentation). Coded characters (s) are arranged in data matrices, which can be transposed and subjected to cladistic analyses to generate intrinsically rooted phylogenetic trees of either molecules or substructures. The trees are then used to generate evolutionary heat maps of secondary structure that color secondary structures or 3D structural models with molecular ancestries. The flow diagram in the right shows the reconstruction of trees of proteomes and trees of protein architectures. A census of domain structures in proteomes of hundreds of completely sequenced organisms is used to compose a data matrix and its transposed matrix, which are then used to build phylogenomic trees describing the evolution of individual architectures and entire molecular repertoires, respectively. Elements of the matrix (g) represent genomic abundances of architectures (at FSF level of hierarchical classification of structure) in proteomes. Ancestries derived from the tree of architectures can be "painted" onto 3D models of the RNase P molecular complex. Evolutionary information from RNA and protein structures is finally combined to generate a model of structural evolution.

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