Table 3.
The percentage of protein-coding transcripts mapped with varying degrees of protein sequence identity by LiftOn, Liftoff, and miniprot
| Experiment | LiftOn (%) (1/≥0.8/≥0.5) |
Liftoff (%) (1/≥0.8/≥0.5) |
miniprot (%) (1/≥0.8/≥0.5) |
|---|---|---|---|
| GRCh38.p14 to CHM13 | 64.4/84.3/84.6 | 64.3/84.2/84.3 | 49.7/82.5/83.4 |
| Human to Pan troglodytes | 17.8/83.5/84.6 | 17.8/82.5/83.2 | 13.4/80.7/82.0 |
| Mus musculus to Rattus norvegicus | 3.6/76.8/83.5 | 3.4/71.8/77.0 | 2.7/72.4/77.4 |
| Drosophila melanogaster to Drosophila erecta | 15.2/81.7/92.0 | 13.2/80.1/90.3 | 10.2/70.0/75.4 |
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Scores are categorized as 100% identity (score = 1), at least 80% identity (score ≥ 0.8), and at least 50% identity (score ≥ 0.5). The comparison evaluates the performance of the programs in mapping annotation from GRCh38.p14 to CHM13, human to P. troglodytes, M. musculus to R. norvegicus, and D. melanogaster to D. erecta.
