Table 4.
Performance of sim4 When Aligning Human mRNAs with the Orthologous Mouse Genomic Sequence
| Gene | 1 | 2 | 3 | 4 | 5 | 6 |
|---|---|---|---|---|---|---|
| ISOT | 91.9 | 98.6 | 20 (20) | 100 | 100 | 0.00 (0/3115) |
| HSENO-2 | 91.7 | 99.1 | 12 (13) | 83.0 | 100 | 1.23 (28/2274) |
| hBAP | 91.3 | 100 | 10 (9) | 100 | 100 | 0.89 (11/1240) |
| GNB3 | 89.8 | 98.2 | 11 (10) | 75.0 | 100 | 0.10 (2/1922) |
| A-2 | 89.5 | 96.8 | 5 (7) | 94.0 | 98.5 | 1.78 (27/1515) |
| HSPTP1CG | 89.2 | 96.1 | 15 (14) | 80.1 | 96.8 | 1.87 (38/2033) |
| HUMDRPLA | 88.9 | 95.1 | 10 (10) | 98.4 | 99.2 | 0.12 (5/4341) |
| C10 | 88.7 | 97.6 | 3 (3) | 78.2 | 100 | 0.00 (0/519) |
| TPI | 88.7 | 96.0 | 7 (7) | 52.9 | 100 | 0.00 (0/1843) |
| C3f | 88.6 | 93.2 | 12 (12) | 100 | 100 | 0.32 (6/1856) |
| C9 | 87.4 | 92.0 | 2 (2) | 98.5 | 100 | 0.11 (1/877) |
| B | 86.4 | 90.9 | 14 (14) | 74.2 | 93.3 | 1.17 (25/2129) |
| C2f | 85.0 | 92.2 | 6 (6) | 72.8 | 100 | 0.23 (2/886) |
| B7 | 81.6 | 86.6 | 7 (5) | 64.2 | 64.4 | 0.33 (4/1208) |
| C8 | 81.5 | 75.9 | 6 (6) | 71.0 | 98.4 | 0.48 (6/1247) |
| CD4 | 70.2 | 62.9 | 10 (7) | 21.0 | 47.3 | 0.59 (18/3051) |
Genes, as named in the left-most column, are taken from data reported by Ansari-Lari et al. (1997, 1998) and sorted according to nucleotide identity. The numbered columns record the following data: (1) Percentage of nucleotide identity between the human and mouse sequences in the protein-coding region. (2) Percentage of amino acid similarity. (Data in columns 1 and 2 are taken from Ansari-Lari et al. 1998.) (3) Number of exons in the gene and, in parentheses, number of putative exons found by sim4. (4) Percentage of the entire mRNA aligned by sim4. (5) Percentage of the protein-coding region aligned by sim4. (6) Percentage of nucleotides aligned by sim4 to positions not in the true mouse mRNA (assuming preservation of splice junctions).