Alignment sensitivity of BLASTP, CS-BLAST, and DELTA-BLAST. Sensitivity measures the fraction of a reference alignment correctly recovered by a sequence alignment. Sequences and their reference alignments from the SABmark superfamily set were used to measure sensitivity. We used only reference alignments with sequence identity below 30% between sequences that did not correspond to SCOP domains present in the training set used to tune DELTA-BLAST parameters. Additionally, we removed reference alignments with fewer than five aligned pairs of residues. The data set contained 10,006 alignments between 2,379 sequences.