TABLE 2.
Selection pressure analysis of ITmD37E- and Vg-C-coding sequences
| Sequence 1 | Sequence 2 | ps | pn | dS | dN | dS/dN | % aa ID |
|---|---|---|---|---|---|---|---|
| AaegITmD37E_Ele4.1 | AgamITmD37E_Ele1.1 | 0.11 | 0.05 | 0.11 | 0.06 | 2.0 | 87.5 |
| AaegITmD37E_Ele4.1 | TambITmD37E_Ele1 | 0.05 | 0.05 | 0.05 | 0.05 | 1.0 | 89.6 |
| AgamITmD37E_Ele1.1 | TambITmD37E_Ele1 | 0.14 | 0.04 | 0.16 | 0.04 | 3.6 | 90.5 |
| AaegVg-C | AgamVg-C | 0.65 | 0.22 | 1.50 | 0.26 | 5.7 | 61.4 |
| AaegVg-C | TambVg-C | 0.72 | 0.21 | 2.52 | 0.24 | 10.5 | 64.4 |
| AgamVg-C | TambVg-C | 0.80 | 0.23 | NAa | 0.28 | NAa | 60.4 |
| AalbVg-C | ApolVg-C | 0.30 | 0.02 | 0.38 | 0.02 | 15.3 | 94.8 |
| OatrVg-C | OepaVg-C | 0.12 | 0.01 | 0.13 | 0.01 | 13.7 | 97.8 |
Manually codon-aligned sequences (see supplemental File S4 at http://www.genetics.org/supplemental/) were used to determine selection pressure by SNAP (http://hcv.lanl.gov/content/hcv-db/SNAP/SNAP.html) (Korber 2000), a program that uses the method of Nei and Gojobori (1986). AgamITmD37E_Ele1.1 and TambITmD37E_Ele1 have intact coding sequences. AaegITmD37E_Ele4.1 has multiple frameshifts that were corrected by codon alignment. Most Vg-C sequences were obtained from Isoe (2000). See supplemental File S1 for methods.
a
SNAP does not give an output for dS when ps > 0.75, indicating substitution saturation.