Research Article
PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets
Table 5
Running time and identification accuracy on the second group of simulated data sets.
| | Sequence # | PairMotifChIP | F-motif | PairMotif+ |
| | 9 | 500 | 14.4 s (0.955) | 7.8 s (0.955) | 68.1 s (0.628) | | 1000 | 60.6 s (0.945) | 17.2 s (0.945) | 410.1 s (0.945) | | 1500 | 133.3 s (0.953) | 27.8 s (0.953) | 989.9 s (0.953) | | 2000 | 231.4 s (0.953) | 40.0 s (0.953) | 1704.1 s (0.953) | | 2500 | 361.4 s (0.951) | 52.8 s (0.951) | 3012.7 s (0.951) | | 3000 | 519.2 s (0.955) | 67.2 s (0.955) | 4307.4 s (0.955) |
| | 15 | 500 | 17.9 s (0.986) | 13581.7 s (0.986) | 14394.4 s (0.986) | | 1000 | 74.8 s (0.983) | 30293.2 s (0.983) | 35172.2 s (0.983) | | 1500 | 150.9 s (0.980) | 50102.5 s (0.980) | — | | 2000 | 253.0 s (0.981) | 66344.7 s (0.981) | — | | 2500 | 396.9 s (0.982) | — | — | | 3000 | 554.4 s (0.981) | — | — |
| | 21 | 500 | 22.9 s (0.995) | — | — | | 1000 | 90.5 s (0.996) | — | — | | 1500 | 171.6 s (0.995) | — | — | | 2000 | 277.2 s (0.995) | — | — | | 2500 | 423.8 s (0.996) | — | — | | 3000 | 592.2 s (0.996) | — | — |
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Note. s: seconds; —: over 24 hours. The number after each running time is the corresponding nucleotide-level identification accuracy nCC.
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