BIOC0003

Six-frame Translation

Given a prokaryotic DNA, RNA or cDNA sequence, you often wish to identify the protein sequence for which it code.

Remember that a codon of 3 DNA bases codes for one amino acid and that DNA is double-stranded. Thus, when trying to translate a given piece of DNA, one must try reading the DNA in each of three possible overlapping reading frames in the forward direction and the complementary strand in the reverse direction. This is known as 6-frame translation and you use a web-based resource to perform a 6-frame translation.

Here is a prokaryotic DNA sequence that you might have obtained in the lab from sequencing:

agtcatgatt aagaaaatcg gtgtgttgac aagcggcggt gatgcgccag gcatgaacgc
cgcaattcgc ggggttgttc gttctgcgct gacagaaggt ctggaagtaa tgggtattta
tgacggctat ctgggtctgt atgaagaccg tatggtacag ctagaccgtt acagcgtgtc
tgacatgatc aaccgtggcg gtacgttcct cggttctgcg cgttgtccgg aattccgcga
cgagaacatc cgcgccgtgg ctatcgaaaa cctgaaaaaa cgtggtatcg acgcgctggt
ggttatcggc gatggcggtt cctacatggg tgcaatgcgt ctgaccgaaa tgggcttccc
gtgcatcggt ctgccgggca ctatcgacaa cgacatcaaa ggcactgact acactatcgg
tttcttcact gcgctgagca ccgttgtaga agcgatcgac cgtctgcgtg acacctcttc
ttctcaccag cctatttccg tggtggaagt gatgggccgt tattgtggag atctgacgtt
ggctgcggcc attgccggtg gctgtgaatt cgttgtggtt ccggaagttg aattcagccg
tgaagacctg gtaaacgaaa tcaaagcggg tatcgcgaaa ggtaaaaaac acgcgatcgt
ggcgattacc gaacatatgt gtgatgttga cgaactggcg catttcatcg agaaagaaac
cggtcgtgaa acccgcgcaa ctgtgctggg ccacatccag cgcggtggtt ctccggtgcc
ttacgaccgt attctggctt cccgtatggg cgcttacgct atcgatctgc tgctggcagg
ttacggcggt cgttgtgtag gtatccagaa cgaacagctg gttcaccacg acatcatcga
cgctatcgaa aacatgaagc gtccgttcaa aggtgactgg ctggactgcg ccgaaaaaat
gtattaatga

Expasy 6-frame translation

Click the following link to access a 6-frame translation server: https://web.expasy.org/translate/

Cut-and-paste the sequence into the server.

Leave all options at their default values and press the appropriate button to submit the sequence to be translated.

You should now have 6 translated sequences, 3 in the forward direction and 3 in the reverse direction.

Note the following features of the translations:

  • The true sequence will always start with a methionine (Met, M) since the start codon (atg) codes for methionine. (Note that codons which code for other amino acids may appear immediately before the start codon.)
  • Stop codons scattered throughout a sequence or individually in the middle of a sequence which otherwise appears to be a coding sequence indicate this is not the correct reading frame
  • The longest coding reading frame will generally be the correct one

Record the correct reading frame

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