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The following files and programs were used to investigate simulated (in silico) codon bias from pseudo-randomly generated sequences versus PCC7120 DNA condon bias. Several large differences were observed between the codon frequencies of the simulated and actual PCC1720 DNA.
CUBseq analyses codon usage bias from RNA-seq data, producing robust CUB estimates that account for variants transcriptome-wide and in highly expressed genes.
Shiny Web app for automatic codon optimization based on codon usage in Strongyloides species, Pristionchus species, Brugia malayi, as well as user-provided custom codon lookup tables
Retrieving nucleotide sequences for PDB and Uniprot structure on a large scale. Analysis of synonymous codons and codon usage on protein structure and evolution.