Table 2 Detection of TE-encoded sequences in SwissProt directly sequenced proteins. The number of SwissProt directly sequenced proteins found with TE protein fragments (from autonomous TEs) by different search programs is shown. The percentage of total SwissProt entries is shown in the parenthesis. The square bracket indicates the number and the percentage of protein entries associated with sequences derived from TEs including the non-autonomous ones.
From: Evaluating the protein coding potential of exonized transposable element sequences
Cut-off value | HMMER | BLASTN | BLASTP | BLASTX | TBLASTN | TBLASTX | RM |
|---|---|---|---|---|---|---|---|
E-value ≤ 1 | 8182 (39.47%) | 2108 (16.39%) [4468: 34.74%] | 2909 (14.03%) | 3030 (14.62%) [4620: 22.28%] | 3418 (26.58%) | 5052 (39.28%) [7576: 58.91%] | N/A |
E-value ≤ 0.1 | 1368 (6.60%) | 655 (5.09%) [1331: 10.35%] | 1481 (7.14%) | 1632 (7.87%) [2185: 10.54%] | 2159 (16.79%) | 3009 (23.40%) [4501: 35.00%] | N/A |
E-value ≤ 0.01 | 214 (1.03%) | 316 (2.46%) [573: 4.46%] | 935 (4.51%) | 1103 (5.32%) [1503: 7.25%] | 1559 (12.12%) | 2180 (16.95%) [3208: 24.95%] | N/A |
E-value ≤ 0.001 | 65 (0.31%) | 187 (1.45%) [351: 2.73%] | 694 (3.35%) | 844 (4.07%) [1186: 5.72%] | 1204 (9.36%) | 1863 (14.49%) [2668: 20.75%] | N/A |
E-value ≤ 0.0001 | 30 (0.14%) | 112 (0.87%) [235: 1.83%] | 516 (2.49%) | 668 (3.22%) [971: 4.68%] | 882 (6.86%) | 1607 (12.50%) [2236: 17.39%] | N/A |
E-value ≤ 0.00001 | 19 (0.09%) | 83 (0.65%) [181: 1.41%] | 372 (1.79%) | 516 (2.49%) [776: 3.74%] | 653 (5.08%) | 1403 (10.91%) [1926: 14.98%] | N/A |
GA (gathering threshold) | 14 (0.07%) | N/A | N/A | N/A | N/A | N/A | N/A |
TC (trusted cut offs) | 14 (0.07%) | N/A | N/A | N/A | N/A | N/A | N/A |
default value | N/A | N/A | N/A | N/A | N/A | N/A | 154 (1.20%) [336: 2.61%] |