Domain enhanced lookup time accelerated BLAST

Biology Direct

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

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)

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.

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