Computational protocol: Design Parameters to Control Synthetic Gene Expression in Escherichia coli

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Protocol publication

[…] All RNA structure strengths are optimal predicted structures calculated using the Vienna RNAfold software package using parameters from Mathews, et al . CAI estimates were calculated as the geometric mean for test gene codons of the ratio of the codon frequency in highly expressed E. coli genes divided by that of the highest frequency codon for each amino acid in those genes . Codon frequencies in highly expressed E. coli genes were taken from EMBOSS . […]

Pipeline specifications

Software tools RNAfold, EMBOSS
Application RNA structure analysis
Organisms Escherichia coli