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Opinion and Comment

Nature Biotechnology 26, 274–275 (1 March 2008) | doi:10.1038/nbt0308-274

BLOSUM62 miscalculations improve search performance

Mark P Styczynski , Kyle L Jensen , Isidore Rigoutsos & Gregory Stephanopoulos

To the editor: The BLOSUM family of substitution matrices, and particularly BLOSUM62, is the de facto standard in protein database searches and sequence alignments. In the course of analyzing the evolution of the Blocks database, we noticed errors in the software source code used to create the initial BLOSUM family of matrices (available online at ftp://ftp.