Step 2: Finding Your Frame
You now have a correctly formatted nucleotide sequence, but what you’re really interested in is the protein sequence. That seems pretty straightforward, since you just have to use a genetic code table to translate your sequence into amino acids by codons, right? Well, it’s not exactly that simple. Gene sequences have what’s called a “frame”, and what frame basically means is that the first nucleotide in your sequence isn’t necessarily the first nucleotide in your gene. Take the sequence AATGACCTGATGGA.
If the sequence reads forward, then any one of these could be the starting nucleotide.
- AATGACCTGATGGA
- AATGACCTGATGGA
- AATGACCTGATGGA
However, if the sequence you really need is in the reverse complement of the sequence you’re looking at, any one of these could also be the starting nucleotide!
- AATGACCTGATGGA
- AATGACCTGATGGA
- AATGACCTGATGGA
Consequently, when considering a brand new nucleotide sequence, you may have to take into account all six frames of a sequence hundreds of bases long to get your amino acid sequence! Luckily, there are sites to help you do this.
- Open BCM SearchLauncher in a new window by right-clicking
- Cut and paste your FASTA-formatted nucleotide sequence into the window
- Select “6 Frame Translation” and hit “Submit”
The server will automatically return to you translations of all six frames. But which is your correct one? There are two basic tips that will help you pick out the correct reading frame:
- Genes should usually go a considerable length without a STOP (*) codon appearing in the middle of them
- Genes usually start with a methionine (M)
So what you should look for is a long, unbroken stretch of amino acids starting with an M. When you have made your selection, move on to the next page.