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Table 1 Effective gap opening penalties for commonly used BLOSUM matrices determined for the benchmark database used

From: Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty

BLOSUM matrix

Gap opening penalty

BLOSUM45

7

BLOSUM50

9

BLOSUM62

11

BLOSUM80

13

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BMC Bioinformatics

ISSN: 1471-2105

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