Table 1 PCAS Annotation Coverage Five motif or domain based algorithms (see text for respective motif or domain databases) were employed in PCAS to annotate proteomes. The annotation coverage by individual algorithms is listed. 1pfscan does not score hits; we skipped frequently matching patterns as well as patterns associated with false SWISSPROT hits [8].
From: PCAS – a precomputed proteome annotation database resource
Algorithms | HMMER | RPS-BLAST | FingerPRINTScan | PSI-BLAST | Pfscan1 |
Parameter Setting | Evalue: 0.05 | Evalue: 0.01 | Evalue: 0.01 | Evalue: 0.01 | |
Arabidopsis (26032): | |||||
Hit number | 18491 | 19499 | 5621 | 12950 | 7090 |
Annotation coverage | 71.0% | 74.9% | 21.6% | 49.7% | 27.2% |
Total | Hits: 20739 | Coverage: 79.7% | |||
Human IPI (47306): | |||||
Hit number | 29601 | 31156 | 13949 | 20887 | 15607 |
Annotation coverage | 62.6% | 65.9% | 29.5% | 44.2% | 33.0% |
Total | Hits: 33407 | Coverage: 70.6% | |||
Mouse IPI (35874): | |||||
Hit number | 25532 | 26575 | 12686 | 17627 | 14145 |
Annotation coverage | 71.1% | 74.0% | 35.3% | 49.1% | 39.4% |
Total | Hits: 28268 | Coverage: 78.7% | |||
Rat IPI (28314): | |||||
Hit number | 20673 | 21350 | 10190 | 14898 | 11014 |
Annotation coverage | 73.0% | 75.4% | 35.9% | 52.6% | 38.8% |
Total | Hits: 22678 | Coverage: 80.1% | |||
Fly (16807): | |||||
Hit number | 11887 | 12412 | 4912 | 8062 | 5205 |
Annotation coverage | 70.7% | 73.8% | 29.2% | 47.9% | 30.9% |
Total | Hits: 13332 | Coverage: 79.3% | |||
Worm (21845): | |||||
Hit number | 14593 | 14667 | 4747 | 8387 | 5581 |
Annotation coverage | 66.8% | 67.1% | 21.7% | 38.3% | 25.5% |
Total | Hits: 16274 | Coverage: 74.4% | |||
S. cerevisiae (6171): | |||||
Hit number | 4133 | 4289 | 1062 | 2695 | 1671 |
Annotation coverage | 66.9% | 69.5% | 17.2% | 43.6% | 27.0% |
Total | Hits: 4517 | Coverage: 73.1% | |||
S. Pombe (5008): | |||||
Hit number | 3714 | 3854 | 962 | 2534 | 1462 |
Annotation coverage | 74.1% | 76.9% | 19.2% | 50.5% | 29.1% |
Total | Hits: 4018 | Coverage: 80.2% |