**2.1. Exploring GenBank for genetic code switches**

Previous Blastp searches found proteins already described in GenBank and aligning with hypothetical peptides translated from randomly chosen frameshifted vertebrate mitochondrial genes. These analyses detected the unusual proteins translated from ORFs of the mitogenome of *Lepidochelys olivacea* [9]. In these cases, the regular mitochondrial proteins are coded in frames that include stops, and hence were not recognized as the regular gene. The annotated frame is stopless, but codes for other, unknown peptides. These other peptides are homologous to peptides translated after frameshift from regular mitochondrial protein coding genes, from other mitogenomes that did not undergo stop codon depletion in non-ORF frames.

#### **2.2. Choice of seed sequences for BLAST searches**

The method described above only detects homologies for sequences sufficiently similar to "seed" sequences used for BLAST analyses of GenBank. Therefore, using as seed the human mitogenome, mainly vertebrate proteins were detected, as for the above-mentioned *Lepidochelys olivacea*. A similar situation occurs for detection of swinger DNA/RNA sequences: the original searches using as seed swinger transformed versions of the human mitogenome only detected vertebrate sequences [45], but BLAST analyses using a randomly chosen invertebrate mitogenome (from the North Pacific krill *Euphausia pacifica* (NC\_016184)) detected numerous additional swinger sequences, from insect mitogenomes [38].

This search principle for insect nucleotide sequences can also be applied for proteins. I use as seed the five peptides translated from the five "noncoding" frames of the 13 regular protein coding genes of *Euphausia*'s previously randomly chosen invertebrate mitogenome. These 65 peptides were blasted to search GenBank for proteins already described and with high homologies with peptides translated from *Euphausia*'s noncoding frames.
