The main caveat in using the programs in this section is to make sure that the correct genetic code is applied to perform the translation or backtranslation. By default, the standard or "universal" code is used; this may not be suitable for mitochondrial sequences, for example.

Another factor to consider when backtranslating a protein sequence is whether to output the most ambiguous nucleotide sequence possible or to use knowledge of the organism's preferred codons to create the most probable nucleotide sequence. The first option is useful if you are trying to identify regions in the nucleotide sequence which have the fewest ambiguities in order to create probes.

Another useful function provided by programs in this section is to find nucleotide substitutions that will add or remove restriction sites from a coding sequence without altering the translation.

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