FIG. 2.
Sensitivity curves for BLAST (B) and FASTA (F) with different scoring matrices (Mat). Matrix B is the traditional BLOSUM62 matrix; E, Q, gtE, gtQ, gtE32, and gtQ32 are described in the text. (A) S. cerevisiae cell wall proteins searched against the yeast proteome and three locally randomized copies of the yeast proteome. Search output was binned into groups of hits by e value (10−130, 10−8, 5 × 10−8, 10−7, 10−5, 5 × 10−2, 10−1, 5 × 10−1, 1, 5, and 10). True positives (yeast ORFs) and false positives (locally randomized yeast pseudoprotein sequences) were counted and plotted for each group of hits. “Gap” is the gap cost (cost to open and cost to extend). For PGP, gtE32, and gtQ32 modifications, the listed gap values were multiplied by 32 before alignments were evaluated. The designated gap penalties gave maximal discrimination for each tested matrix.