Table 4.
Performance test of eukaryotic genome annotation tools based on four species
| Species | Software | Genes | CDS | CDS with function | CDS without function | rRNA | tRNA | Genes with same start and end position (%)a | Genes with same start position | Similarity scoreb |
|---|---|---|---|---|---|---|---|---|---|---|
| Plasmodium falciparum | Ref_annotationc | 5457 | 5354 | 3616 (67.54%) | 1738 (32.46%) | 28 | 45 | / | / | / |
| Companion_web | 5196 | 5130 | 3072 (59.89%) | 2058 (40.11%) | 14 | 47 | 5009 (91.80%) | 5027 (92.12%) | 94.38% | |
| Companion_cl | 4521 | 4392 | 2672 (60.84%) | 1720 (39.16%) | 19 | 46 | 4317 (79.11%) | 4345 (79.62) | 87.09% | |
| GeneSAS_genemarkES | 5184 | 5108 | / | / | 14 | 62 | 3929 (72.00%) | 4388 (80.41%) | 82.47% | |
| GAL | 1706 | 1706 | 1362 (79.84%) | 344 (20.16%) | / | / | 323 (5.92%) | 753 (13.80%) | 21.02% | |
| GAAP | 5377 | 5377 | / d | / | / | / | 2799 (51.30%) | 3657 (67.01%) | 67.51% | |
| Toxoplasma gondii | Ref_annotation | 8925 | 8292 | 4008 (48.34%) | 4284 (51.66%) | 424 | 183 | / | / | / |
| Companion_web | 4996 | 4488 | 2441 | 508 | 301 | 193 | 1639 (18.36%) | 1976 (22.14%) | 28.39% | |
| Companion_cl | 11 297 | 10 520 | 2151 (20.45%) | 8369 (79.55%) | 566 | 191 | 1067 (12.06%) | 1488 (16.67%) | 14.72% | |
| GeneSAS_genemarkES | / | / | / | / | / | / | / | / | / | |
| GAL | 34 288 | 34 288 | 27 368 (79.82%) | 6920 (20.18%) | / | / | 116 (1.30%) | 796 (8.92%) | 3.68% | |
| GAAP | 26 204 | 26 204 | / | / | / | / | 96 (1.08%) | 545 (6.11%) | 3.10% | |
| Babesia microti | Ref_annotation | 3685 | 3567 | 2335 (65.46%) | 1232 (34.54%) | 16 | 68 | / | / | / |
| Companion_web | 3151 | 3075 | 1 (0.03%) | 3074 (99.97%) | 8 | 64 | 2262 (61.38%) | 2642 (71.70%) | 77.30% | |
| Companion_cl | 2655 | 2572 | 1474 (57.31%) | 1098 (42.69%) | 8 | 63 | 2461 (66.78%) | 2507 (68.03%) | 79.09% | |
| GeneSAS_genemarkES | 3066 | 3066 | / | / | / | / | 2427 (65.86%) | 2740 (74.36%) | 81.17% | |
| GAL | 2104 | 2104 | 2031 (96.53%) | 73 (3.5%) | / | / | 710 (19.27%) | 1200 (32.56%) | 41.46% | |
| GAAP | 1712 | 1712 | / | / | / | / | 466 (12.65%) | 852 (23.12%) | 31.57% | |
| Aspergillus fumigatus | Ref_annotation | 9859 | 9630 | 6977 (72.45%) | 2653 (27.55%) | / | 229 | / | / | / |
| Companion_web | / | / | / | / | / | / | / | / | / | |
| Companion_cl | / | / | / | / | / | / | / | / | / | |
| GeneSAS_genemarkES | 9706 | 9706 | / | / | / | / | 6147 (62.35%) | 7424 (75.30%) | 75.89% | |
| GAL | 8978 | 8978 | 8623 (96.05%) | 355 (4%) | / | / | 6150 (62.38%) | 7250 (73.54%) | 76.98% | |
| GAAP | 8681 | 8681 | / | / | / | / | 5908 (59.92%) | 7036 (71.37%) | 75.90% |
aPercentage is equal to (genes with same start and end position/Ref_annotation genes)*100.
bSimilarityScore = ((genes with same start position)/(Totalx + Totalz))*2*100. Totalx and Totalz are the total numbers of genes in the software annotation and reference annotation. The function is from BEACON (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4539851/).
cref_annotation means the reference annotation. It is from NCBI RefSeq.
dThe blank is here because the commercial tool CloudBlast is required for functional annotation.