Number of true positives vs. number of false positives for DELTA-BLAST, CS-BLAST and BLASTP. The searched database was created using ASTRAL 40 sequences for SCOP version 1.75. To create the query set, we sorted the SCOP domains in lexicographic order and selected even numbered sequences for the test query set. We excluded from the query set any sequence that was the sole member of its superfamily in ASTRAL 40. We considered a query and database sequence to be homologs if they belonged to the same superfamily, and non-homologs if they belonged to different folds. The search results generated by all queries were pooled and ordered by E-value. The database and the query set consisted of 10,569 and 4852 sequences, respectively.