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Reverse Translation and Handling Ambiguous Characters
The Reverse Translation tool allows you to convert (reverse translate) an amino acid sequence to a DNA sequnce. Due to the degeneracy of the code (there are 64 different codons and only 20 amino acids), this process results in degenerate or ambiguous code. Unlike most other sequence analysis programs, Expression extensively supports ambiguous characters in most of its functions. In addition, Expression can also handle ambiguous amino acids in protein sequences, such as those created in the consensus sequence of a multiple alignment. To understand how Expression deals with ambiguity within a particular tool, please refer to its corresponding tutorial.
Reverse Translation
Couldn't be simpler - just load in your sequence, and select the RevTrans tool. A pane will appear at the bottom of the Sequence Editor which contains the reverse translation of the current amino acid sequence. You can actually edit or paste further sequence information, and the reverse translation will occur in real-time. To create a new DNA document from the reverse translation for further analysis, simply push the Make Document button.
Notation for Ambiguous Characters
Expression handles both ambiguous DNA and amino acid characters. Ambiguous DNA characters (bases) are represented using the standard notation recommended by the International Union of Biochemistry:
| R = A or G | S = G or C | V = A or C or G |
| Y = C or T | W = A or T | D = A or G or T |
| M = A or C | H = A or C or T | N = A or C or G or T |
| K = G or T | B = C or G or T |
For example:
ACTRATCTAACGATCGATCT
would signify that the fourth base could be either guanine (G) or thymine (T).
Ambiguous amino acids are bracketed and olive coloured. For example:
ML(VIL)TGAGTRYFPPILAGWG
would signify that the third residue could be either valine (V), isoleucine (I) or leucine (L).
Related Articles
Using the Sequence Map
Annotating Your Sequences
Restriction Mapping and Analysis
Finding Patterns and Motifs in DNA or Protein Sequences
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