Computational protocol: Evolution of Chaperonin Gene Duplication in Stigonematalean Cyanobacteria (Subsection V)

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Protocol publication

[…] The search for GroES/GroEL homologs was performed with BLAST+ () using the amino acid sequence of GroES and GroEL encoded in Escherichia coli K12 MG1655 as a query. The search database included all sequenced cyanobacterial genomes in NCBI RefSeq (ver. July 2014) () and Joint Genome Institute (JGI; ). An e-value <10− 10 was used as a sequence similarity threshold. Annotations of the BLAST hits were determined manually according to RefSeq database. Hits that lacked an annotation were validated by reBLASTing against NCBI. Multiple sequence alignments of the GroES/GroEL orthologs were computed with MAFFT ver. 7.027b (). Phylogenetic trees were reconstructed using PhyML ver. 3.1 with the Le-Gascuel (LG) substitution model () for amino acid sequences and general time-reversible (GTR) substitution model () for nucleotide sequences and SPR search algorithm (). Testing hypotheses regarding the tree topology was performed by reconstructing a maximum-likelihood tree with a user tree constraint. The comparison of ML phylogeny and the constrained phylogeny was performed using CONSEL ver. 1.2 (). The calculation of synonymous (dS) and nonsynonymous (dN) substitution rates was performed with CodeML (). Codon alignments for the dN/dS calculation were prepared with PAL2NAL (). Phylogenetic trees were plotted with FigTree (http://tree.bio.ed.ac.uk/software/figtree/). […]

Pipeline specifications

Software tools MAFFT, PhyML, CONSEL, PAML, PAL2NAL, FigTree
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Escherichia coli