Table 3 True negative ortholog test set and ortholog predictions of GreenPhyl (GP), Inparanoid (INP) and BBMH (BH).
From: Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants
Arabidopsis thaliana | Oryza sativa | Literature | UP prediction | |||||
|---|---|---|---|---|---|---|---|---|
TAIR id | Alias | TIGR id | Alias | UP | PMID | GP | BBMH | INP |
- | - | Os03g11614.1 | LHS1 | 0/3 | 16099195; 10852934 | 0/3 | 0 | 0 |
- | - | Os06g06750.1 | MADS5 | Â | Â | Â | Â | Â |
- | - | Os03g54170.1 | MADS34 | Â | Â | Â | Â | Â |
At5g10140.1 | FLC | - | - | 6/0 | 12667866;12724541; 15695584 | 6/0 | 0 | 0 |
At5g65060.2 | MAF3 | - | - | Â | Â | Â | Â | Â |
At5g65070.1 | MAF4 | - | - | Â | Â | Â | Â | Â |
At5g65050.1 | MAF2 | - | - | Â | Â | Â | Â | Â |
At1g77080.3 | MAF1 | - | - | Â | Â | Â | Â | Â |
At5g65080.1 | MAF5 | - | - | Â | Â | Â | Â | Â |
At3g18990.1 | VRN1 | - | - | 2/0 | 12667866;16549797 | 2/0 | 1/1 | 1/2 |
At1g49480.1 | RTV1 | - | - | Â | Â | Â | Â | Â |
At4g16845.1 | VRN2 | - | - | 1/0 | 12667866 | 1/0 | 0 | 0 |