Computational protocol: Comparative genomics of regulation of heavy metal resistance in Eubacteria

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Protocol publication

[…] COG0789 proteins were retrieved from the SMART database (domain accession number SM00422) []. Multiple sequence alignments were done using the ClustalX program []. Phylogenetic trees were constructed using the PROML program from the PHYLIP package (implementing the maximum likelihood algorithm) []. The GenomeExplorer package [] was used to construct recognition profiles and to identify candidate regulatory sites in genomic sequences. […]

Pipeline specifications

Software tools Clustal W, PHYLIP
Application Phylogenetics
Chemicals Cadmium, Copper, Glutathione, Mercury, Zinc