Computational protocol: Evolution of Mitochondria Reconstructed from the Energy Metabolism of Living Bacteria

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[…] To identify genes and their products with others currently present in National Center for Biotechnology Information (NCBI) resources, we have extensively used the program DELTABLAST, Domain Enhanced Lookup time Accelerated BLAST , integrated with hydropathy analysis conducted with in house algorithms or the program WHAT (Web-based Hydropathy, Amphipathicity and Topology http://saier-144-21.ucsd.edu/barwhat.html ). Manually refined alignments of bioenergetic proteins were subjected to phylogenetic analysis with maximum likelihood algorithm and 100 bootstrap resamplings, using the program PhyML 3.0 and evolutionary models selected with Prottest3, as described earlier . The results obtained with this rigorous method essentially matched those obtained with the recent options of DELTABLAST (cf. ). The genomes of Asaia platicody and Saccharibacter sp. (EMBL accession: CBLX010000001/27 and CBLY010000001/09, respectively) were recently reported by Chouaia et al . See Supporting Information for additional methods and procedures of gene recognition, operon classification (cf. ) and sequence analysis of proteins (cf. , , ). […]

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