Computational protocol: In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae

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Protocol publication

[…] Protein sequences coding for GroEL1 (Ct110), GroEL2 (Ct604) and GroEL3 (Ct755) were retrieved from the GeneBank database for the different species of Chlamydiae. The sequences, species names and the protein-coding sequence accession numbers are provided in table of additional file . We aligned protein sequences using the program ClustalX [] with the default settings. We then aligned nucleotide sequences concatenating triplets of nucleotides according to the multiple protein sequence alignment (alignments are available from the authors on request). Together with the groEL gene sequence we also obtained alignments for client proteins shown to depend on E. coli GroEL to acquire a productive (functional) protein conformation []. We obtained the sequences for each one of the Chlamydiae species or strains from GenBank and the accession numbers are provided in Table of additional file . We then aligned the sequences for each one of the protein-coding genes following the same procedure detailed above.Regarding phylogenetic analyses, for each one of the multiple sequence alignments we first used ModelTest 1.3 [] to determine the best candidate substitution rate matrix for maximum likelihood inference. The program pinpointed TrN + I + G as first option. We used then the output generated by ModelTest as input for the program PAUP [] and inferred a maximum-likelihood phylogenetic tree for the alignment containing the three different GroEL protein-coding sequences using the heuristic approach. […]

Pipeline specifications

Software tools Clustal W, ModelTest-NG, PAUP*
Application Phylogenetics
Diseases Chlamydia Infections