BLOSUM

BLOSUM stands for BLOcks SUbstitution Matrix.

BLOSUM works better than the PAM matrices for distantly related sequences.

[edit] 1 Weighting by clustering

Multiple contributions to amino acid pair frequencies from closely related members of a family were reduced by clustering the sequences in blocks weighted as a single sequence in counting pairs. Blocks were formed by grouping together sequence segments at a given percent identity or higher. If a sequence has a percent identity with any clustered sequence equal to or higher than the cutoff, it is included in that cluster.

The number in a BLOSUM matrix's name stands for the percent identity cutoff for the blocks. So BLOSUM80's clusters are composed of sequences at or above 80% identity, and BLOSUM62's clusters are composed of sequences at or above 62%.

[edit] 2 Links

• Nature: Where did the BLOSUM62 alignment score matrix come from?
• BLOCKS server

[edit] 3 References

• Amino acid substitution matrices from protein blocks
• Henikoff S, Henikoff JG. Automated assembly of protein blocks for database searching. Proc Natl Acad Sci U S A. 1992 November 15; 89(22): 10915–10919.