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Reverse Translation
A protein sequence can be back-translated into DNA. Due to degeneracy of the genetic code every amino acid could translate into several different codons (only 20 amino acids but 64 different codons). Thus, the program offers a number of choices for determining which codons should be used.
CLC's workbenches include codon frequency tables for a large number of species, making it possible to make species-specific reverse translations. You can translate several protein sequences at a time.
The program offers these three different ways of performing the reverse translations:
- Most frequently used codon. On the basis of the selected translation table, this will assign the codon that occurs most often. When choosing this option, the results of performing several reverse translations will always be the same, contrary to the following two options.
- Uniform distribution. This will randomly back-translate an amino acid to a codon without using the translation tables. Every time you perform the analysis you will get a different result.
- Distribution according to frequency. This option is a mix of the other two options. The selected translation table is used to attach weights to each codon based on its frequency. The codons are assigned randomly with a probability given by the weights. A more frequent codon has a higher probability of being selected. Every time you perform the analysis, you will get a different result. This option yields a result that is closer to the translation behavior of the organism (assuming you chose an appropriate codon frequency table).
The Codon Frequency Table is used to determine the frequencies of the codons. Select a frequency table from the list that fits the organism you are working with. A translation table of an organism is created on the basis of counting all the codons in the coding sequences.
Every codon in a Codon Frequency Table has its own count, frequency (per thousand) and fraction which are calculated in accordance with the occurrences of the codon in the organism.
When the translation has been performed, the newly created nucleotide sequence is shown, and if the analysis was performed on several protein sequences, there will be a corresponding number of views of nucleotide sequences.
