Talk:BLOSUM

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[edit] BLOSUM62: more or less than 62% identity?

"The Henikoffs took a big database of trusted alignments (their BLOCKS database), and (in effect) only counted pairwise sequence alignments related by less than some threshold percentage identity. A threshold of 62% identity or less resulted in the target frequencies for the BLOSUM62 matrix. An 80% threshold gave the more highly conserved target frequencies of the BLOSUM80 matrix, and a 45% threshold gave the more divergent BLOSUM45 matrix."

Source: Sean R. Eddy, Where did the BLOSUM62 alignment score matrix come from? Nature Biotechnology 22, 1035--1036 (2004) doi:10.1038/nbt0804-1035

http://www.nature.com/nbt/journal/v22/n8/full/nbt0804-1035.html

"In order to avoid over-weighting closely-related sequences, the Henikoffs replaced groups of proteins that have sequence identities higher than a threshold by either a single representative or a weighted average. The threshold of 62% produces the commonly used BLOSUM62 substitution matrix."

Source: Arthur M. Lesk, Introduction to Bioinformatics Oxford University Press, 2002, p.175

Winterschlaefer 15:52, 14 February 2007 (UTC)

For what I know a BLOSUM62 matrix is good for alignements which have 62% or MORE identity XApple 00:32, 25 February 2007 (UTC)