BLOSUM

thumb|400px|The BLOSUM62 matrix, the amino acids have been grouped and coloured based on Margaret Dayhoff|Margaret Dayhoff's classification scheme. Positive and zero values have been highlighted. In bioinformatics, the BLOSUM (BLOcks SUbstitution Matrix) matrix is a substitution matrix used for sequence alignment of proteins. BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences. They are based on local alignments. BLOSUM matrices were first introduced in a paper by Steven Henikoff and Jorja Henikoff. They scanned the BLOCKS database for very conserved regions of protein families (that do not have gaps in the sequence alignment) and then counted the relative frequencies of amino acids and their substitution probabilities. Then, they calculated a log-odds score for each of the 210 possible substitution pairs of the 20 standard amino acids. All BLOSUM matrices are based on observed alignments; they are not extrapolated from comparisons of closely related proteins like the PAM Matrices.

==Biological background== The genetic instructions of every replicating cell in a living organism are contained within its DNA. Throughout the cell's lifetime, this information is transcribed and replicated by cellular mechanisms to produce proteins or to provide instructions for daughter cells during cell division, and the possibility exists that the DNA may be altered during these processes. This is known as a mutation. At the molecular level, there are regulatory systems that correct most — but not all — of these changes to the DNA before it is replicated.