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Table 2 Results of Experiments 1–5.

From: Fast index based algorithms and software for matching position specific scoring matrices

Experiment 1: 4,034 PSSMs in 20.2 MB protein sequences
p-value DN00 (total time) DN00 (search) LAsearch ESAsearch +41 sec.
10-10 65,808 64,939 39,839 41,813
10-20 38,773 37,706 23,786 24,378
10-30 21,449 20,362 14,111 13,084
10-40 9,606 8,533 8,067 5,374
Experiment 2: 220 PSSMs in 37.2 MB DNA
MSS MatInspector LAsearch ESAsearch +32 sec.
0.80 12,773 3,605 202
0.85 12,567 3,189 108
0.90 12,487 2,818 53
0.95 12,445 2,356 12
1.00 12,429 885 1
Experiment 3: 11,411 PSSMs in 4.3 MB protein sequences
E-value FingerPrintScan LAsearch ESAsearch +10.2 sec.
10-10 4,733 3,423 1.244
10-20 4,710 486 52
10-30 4,706 27 10
Experiment 4: 576 PSSMs in 162.9 MB DNA
MSS    LAsearch ESAsearch +586 sec.
0.85    18,446 318
0.90    16,376 150
0.95    13,764 50
1.00    5,294 1
Experiment 5: 28,337 PSSMs in 4.3 MB protein sequences
raw-th Blimps LAsearch ESAsearch +10.2 sec.
945 271:30:16 16:03:12 11:35:58
  1. Experiment 1: Running times in seconds of the different PSSM searching methods at different levels of stringency, when searching for 4,034 amino acid PSSMs in 59,021 sequences (21.2 MB) from SwissProt. These are the same PSSMs and sequences used in the experiments of [13]. Experiment 2: Running times in seconds of MatInspector, LAsearch, and ESAsearch, when searching 220 PSSMs on both strands of 37.2 MB DNA sequence data at different matrix similarity score (MSS) cutoffs. Experiment 3: Running times in seconds of FingerPrintScan, LAsearch, and ESAsearch when searching all 11,411 PSSMs from the PRINTS database in the RCSB protein data bank (PDB) for different E-values. Experiment 4: Running times in seconds of LAsearch and ESAsearch when searching 576 PSSMs in H. sapiens chr. 6 at different matrix similarity score (MSS) cutoffs. Experiment 5: Running times in hh:mm:ss of Blimps, LAsearch, and ESAsearch when searching all 28,337 PSSMs from the BLOCKS database in PDB. We used a raw score threshold of 945 as suggested in the Blimps documentation for searching large databases. For each experiment, the additional time needed for the construction of the enhanced suffix array is shown in the head of the ESAsearch column.