A sequence translated using three different genetic codes illustrating changes in BLASTx scores.

The nucleotide sequence from comp102324 was translated as a query under three different genetic codes with the dashes (-) representing identically translated codons. The top amino acid translation uses NCBI genetic code 1, where UGA, UAA, and UAG are all interpreted as stop (*). These codons are shown above the amino acid translation and are boxed. The NCBI genetic code 4 translates UGA as tryptophan (W), increasing the number of pairwise identities in this example by three, and the number of positive matches by one (identified in the midline with +). However, three UAA stop codons still interrupt the open reading frame. The third translation using NCBI code 6 interprets UAA and UAG as glutamine (Q), which does not increase the number of pairwise identities, but does increase the number of positives, or similar amino acids by two. In this example there are no UAG codons. The top blast hit (Candida tenuis ATCC10573 gi 575519749) and pairwise identities or positives when translating all three stop codons as amino acids are shown below the different translations.