Reading frames and the genetic code
How the ribosome reads mRNA in triplets, why the reading frame matters, and what the start and stop codons actually do.
What a reading frame is
Because codons are exactly three bases long, any stretch of RNA can be read in three different frames depending on where you start: at the first base, the second, or the third. Each frame produces a completely different string of amino acids, and only one usually spells out the intended protein. Slip the start by a single base and the message becomes gibberish, often peppered with premature stops. This is why a one-base insertion or deletion, called a frameshift, can be so damaging to a gene. This translator always begins at the first base you paste, so choosing the frame is up to you.
Start codons and where translation begins
In living cells the ribosome does not start translating at a random spot. It scans the messenger RNA and typically begins at the first AUG in a favourable context, which sets the reading frame for everything downstream. AUG codes for methionine, so most freshly made proteins start with a methionine that may later be trimmed off. A few organisms use alternative start codons such as GUG or UUG, but table 1 treats AUG as the canonical start. If you want the tool to mimic the cell, trim your sequence so it begins at the AUG you care about.
The three stop codons
Translation ends when the ribosome reaches one of three stop codons: UAA, UAG or UGA. These do not code for an amino acid; instead they recruit release factors that free the finished protein. The three have nicknames from classic genetics, ochre (UAA), amber (UAG) and opal (UGA), a legacy of the mutants used to discover them. In this tool a stop is shown in the three-letter column as Stop and as an asterisk in the one-letter protein string. Turning off 'stop at first stop codon' lets you see whether more codons follow, which matters when checking read-through or a longer open reading frame.
DNA, mRNA and the T to U swap
Genes are stored as DNA, which uses thymine (T), while the messenger copy the ribosome reads uses uracil (U) in the same positions. The genetic code is written in RNA codons, so translating DNA means treating each T as a U. Ticking the DNA option does exactly that before lookup. Remember to supply the coding strand, the one that reads the same as the mRNA, rather than the complementary template strand, or the result will be the translation of the wrong sequence.