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Table 5 BLAST Substitution Matrices and Gap Costs used for BLASTP searches in this paper.

From: HomPPI: a class of sequence homology based protein-protein interface prediction methods

Query Length Substitution Matrix Gap Costs
<35 PAM-30 (9,1)
35-50 PAM-70 (10,1)
50-85 BLOSUM-80 (10,1)
85 BLOSUM-62 (10,1)