Table 1 Descriptions of protein datasets. # Seq. gives the number of input protein sequences. Length gives the length of the protein motif searched for. |V| gives the number of vertices in the original graph constructed from the dataset. DEE gives the methods used to prune the graph, and are denoted by (1) clique-bounds DEE, (2) tighter constrained bounds and (3) graph decomposition. |V DEE | is the number of vertices in the graph after pruning. E-value lists the e-value of the motif found by the LP/DEE algorithm.
From: A combinatorial optimization approach for diverse motif finding applications
Dataset | # Seq. | Length | |V| | DEE | |V DEE | | E-value |
|---|---|---|---|---|---|---|
Lipocalin | 5 | 16 | 844 | (1) | 5 | 3.80 × 10-16 |
Helix-Turn-Helix | 30 | 20 | 6870 | (1,2,3) | 260 | 3.88 × 10-67 |
Tumor Necrosis Factor | 10 | 17 | 2329 | (1) | 10 | 1.50 × 10-40 |
Zinc Metallopeptidase | 10 | 12 | 7761 | (1,2) | 10 | 5.82 × 10-23 |
Immunoglobulin Fold | 18 | 10 | 7498 | (1,2,3) | 187 | 3.04 × 10-24 |