Bayesian Decomposition Analysis of Bacterial Phylogenomic Profiles

 


Ghislain Bidaut1,2, Karsten Suhre2, Jean-Michel Claverie2, Michael F. Ochs1

1: Fox Chase Cancer Center, Bioinformatics, Department of Information Science and Technology, Philadelphia, PA, 19111, USA
2: Structural and Genomic Information Laboratory, (CNRS UPR2589), 13402 Marseille, France



This page contains supplemental information related to the publication "Bayesian Decomposition Analysis of Bacterial Phylogenomic Profiles", submitted to The American Journal of Pharmacogenomics.

ClutrFree is available here and Bayesian Decomposition here.

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1 Generation of the phylogenomic profiles


Generation of the Phylogenomic Profiles

Generation of the phylogenomic profiles: 1073 mutual homologs of E.coli and M.tuberculosis, have been selected and scored with BLAST against the genome sequence of 31 bacteria of interest, yielding 1073 profiles of size 31.


2 Results and patterns found in the data



Patterns found in the Data


This figure shows a few pattern vectors obtained by BD and plotted with ClutrFree for a decomposition in k=30 vectors. BD has revealed the bacterial phylogeny for Actinobacteria, Firmicutes and other genuses such as Chlamydiae, Rickettsia and Spirochetes. All Actinobacteria have been grouped in one single pattern and also separated in many patterns . The thickness of the lines is proportional to the stability of each bacteria along the tree branch to which it belongs.