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Table 3 Retrieval accuracy for DELTA-BLAST, BLASTP, CS-BLAST, and 5 iterations of PSI-BLAST and CSI-BLAST, across SCOP classes

From: Domain enhanced lookup time accelerated BLAST

Class BLASTP CS-BLAST DELTA-BLAST PSI-BLAST CSI-BLAST
A 0.061 (0.0003) 0.084 (0.0005) 0.192 (0.0009) 0.172 (0.0008) 0.192 (0.0012)
B 0.095 (0.0003) 0.108 (0.0004) 0.356 (0.0013) 0.285 (0.0022) 0.267 (0.0028)
C 0.062 (0.0002) 0.096 (0.0009) 0.189 (0.0015) 0.163 (0.0013) 0.173 (0.0015)
D 0.166 (0.0004) 0.198 (0.0007) 0.471 (0.0009) 0.443 (0.0009) 0.452 (0.0008)
E 0.263 (0.0013) 0.276 (0.0011) 0.459 (0.0046) 0.415 (0.0023) 0.439 (0.0029)
F 0.376 (0.0026) 0.391 (0.0034) 0.563 (0.0029) 0.474 (0.0019) 0.530 (0.0072)
G 0.066 (0.0010) 0.059 (0.0014) 0.120 (0.0010) 0.133 (0.0010) 0.123 (0.0021)
  1. We divided the pooled search results into subsets, according to the SCOP protein class of the query and computed ROC n scores for each subset, with n equal to the number of queries in each class. See the legend of Figure 2 for data set description. The rows represent SCOP protein classes: A - All alpha proteins (866 queries), B - All beta proteins (1034 queries), C - Alpha and beta proteins a/b (1310 queries), D - Alpha and beta proteins a + b (1219 queries), E - Multi-domain proteins (78 queries), F - Membrane and cell surface proteins and peptides (64 queries), and G - Small proteins (284 queries). The columns show ROC n scores and standard errors for each method. The largest scores per row are in bold font.