The rule to translate nucleotide sequence into amino acid sequence is specified in accordance with agreements of International Nucleotide Sequence Database Collaboration.
The codon table using a CDS feature is specified in the value of /transl_table qualifier as a number of The Genetic Codes.
There are three points frequently misunderstood.
- You should specify /organelle qualifier to assign correct genetic code for mitochondrion or chloroplast.
- The initiation codon is M, Met, methyonine, not G or V.
See Start codon and N-Formylmethionine - When an amino acid can be specified by two bases (i.e. degeneracy of codons), it will be outputted.
There are some exceptional cases, represented by RNA editing and so on.