MacVectorTip: Create custom Codon Usage Tables for ORF analysis and reverse translation

MacVector uses codon usage tables (also called “Codon Bias”) to help you predict protein coding regions in the Analyze | Nucleic Acid Analysis Toolbox functions and also the protein Analyze | Reverse Translation... function. For example, here are the Plus and Minus strand Staden Codon Preference plots aligned under the Plus/Minus ORFs for a Streptomyces coelicolor cosmid fragment using the Streptomyces coelicolor.bias codon usage file.

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While MacVector includes a collection of common codon usage tables (Human, Mouse, Drosophila, E. coli etc.) in the /MacVector/Codon Bias Tables/ folder, there may be times when you need a custom table. We do have a utility that can convert data in the appropriate format into a MacVector .bias file, but unfortunately it will not yet run on recent macOS releases. However, we are happy to generate these files for you if you send us the raw data. To do this, go to http://www.kazusa.or.jp/codon/ and search for your preferred organism. You should ask to see the data in the CodonFrequency GCG format.

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Copy the text starting from AmAcid to the end of the data.

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Paste it into an email and send it to support@macvector.com and we will send you back a .bias file.

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