Table 2.
Nomenclature for Overlapping Protein-Coding Reading Frames.
| Studya | Frameb |
|||||
|---|---|---|---|---|---|---|
| 5′- 123123 -3′ | 5′- 123 -3′ | 5′- 123 - 3′ | 5′- 123 -3′ | 5′- 123 -3′ | 5′- 123123 -3′ | |
| 5′- 123123 -3′ | 5′- 123123 -3′ | 5′- 123123 -3′ | 3′- 321321 -5′ | 3′- 321321 -5′ | 3′- 321321 -5′ | |
| OLGenie; Wei and Zhang (2015) | Reference (ss11) | ss12 | ss13 | sas11 | sas12 | sas13 |
| Scherer et al. (2018) | +1 | +3 | +2 | −3 | −2 | −1 |
| Lèbre and Gascuel (2017) | +0 | +2 | +1 | −1 | −2 | −0 |
| Schlub et al. (2018) | +0 | +2 | +1 | −c2 | −c1 | −c0 |
| Sabath et al. (2008) | 0 | 2 (same-strand) | 1 (same-strand) | 1 (opposite-strand) | 2 (opposite-strand) | 0 (opposite-strand) |
| Belshaw et al. (2007) | 0 | −1 | +1 | rc-1 | rc+1 | rc0 |
| Firth and Brown (2006) c | 0 | +2 | +1 | −1 | −2 | −3 |
| Rogozin et al. (2002) c | − | − | − | C1 | C3 | C2 |
| Krakauer (2000) c | − | +2 | +1 | −1 | 0 | −2 |
| Smith and Waterman (1980) c | 0 | 2 | 1 | 5 | 3 | 4 |
a
Studies in descending order by year of publication.
b
Black denotes the reference frame and blue denotes the alternate frame; one alternate codon position is underlined to show overlap with reference codon position 1 (e.g., position 3 for ss13).
c
As reported by Lèbre and Gascuel (2017).