Computational protocol: Novel Metabolic Attributes of the Genus Cyanothece, Comprising a Group of Unicellular Nitrogen-Fixing Cyanobacteria

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Protocol publication

[…] Orthologous sets of proteins were identified across 61 cyanobacterial strains through an all-versus-all BLASTP v2.2.23 (, ) analysis of their respective proteomes. Orthology was defined as reciprocal best-match hits between proteomes, matching 66% of the length of the longer of the two proteins, with scores 1/10 of the higher of the self-self scores. Any highest-scoring protein with multiple identically scoring hits was discarded. Sets of orthologs were considered to be conserved if ≥ 75% of proteins within the set were orthologous to one another, resulting in 226 sets of genes with orthologs in all 61 proteomes. Each of the 226 sets of 61 proteins was individually aligned using the MAFFT v6.811b software program () and then concatenated into a single alignment, removing all columns containing gaps. The PHYLIP v3.64 () software package was used to generate the final consensus tree using the Fitch-Margoliash method with 100 bootstraps, global rearrangement, and 1 jumble per bootstrap. Distances were then back fit to the resulting consensus tree using maximum-likelihood estimates from the original concatenated alignment. The resultant tree was rendered using the Archaeopteryx v0.957b software program (). [...] Whole-genome alignments were performed using “ProgressiveMauve” () with default parameter values. […]

Pipeline specifications

Software tools BLASTP, MAFFT, Archaeopteryx, Mauve
Applications Phylogenetics, Nucleotide sequence alignment
Chemicals Carbohydrates, Carbon, Nitrogen, Oxygen