05-04-2012, 02:49 PM
BLOSUM Matrices
BLOSUM_matrices.ppt (Size: 329 KB / Downloads: 145)
BLOSUM matrices
Blocks Substitution Matrix. Scores for each position are obtained frequencies of substitutions in blocks of local alignments of protein sequences [Henikoff & Henikoff92].
For example BLOSUM62 is derived from sequence alignments with no more than 62% identity.
BLOSUM Scoring Matrices
BLOck SUbstitution Matrix
Based on comparisons of blocks of sequences derived from the Blocks database
The Blocks database contains multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins (local alignment versus global alignment)
BLOSUM matrices are derived from blocks whose alignment corresponds to the BLOSUM-,matrix number
Comparison
PAM is based on an evolutionary model using phylogenetic trees
BLOSUM assumes no evolutionary model, but rather conserved “blocks” of proteins