24-09-2013, 02:35 PM
Differences between PAM and BLOSSUM
PAM and BLOSSUM[.doc (Size: 34.5 KB / Downloads: 17)
INTRODUCTION
PAM matrices are based on an explicit evolutionary model (that is, replacements are counted on the branches of a phylogenetic tree), whereas the Blosum matrices are based on an implicit rather than explicit model of evolution.
The sequence variability in the alignments used to count replacements. The PAM matrices are based on mutations observed throughout a global alignment, this includes both highly conserved and highly mutable regions. The Blosum matrices are based only on highly conserved regions in series of alignments forbidden to contain gaps.
The method used to count the replacements is different, unlike the PAM matrix, the Blosum procedure uses groups of sequences within which not all mutations are counted the same.
PAM (Point Accepted Mutation) matrix
Amino acid scoring matrices are traditionally PAM (Point Accepted Mutation) matrices which refer to various degrees of sensitivity depending on the evolutionary distance between sequence pairs. In this manner PAM40 is most sensitive for sequences 40 PAMs apart. PAM250 is for more distantly related sequences and is considered a good general matrix for protein database searching. For nucleotide sequence searching a simpler approach is used which either convert a PAM40 matrix into match/mismatch values which takes into consideration that a purine may be replaced by a purine and a pyrimidine by a pyrimidine.
e.g. The PAM 250 matrix
This is appropriate for searching for alignments of sequence that have diverged by 250 PAMs, 250 mutations per 100 amino acids of sequence. Because of back mutations and silent mutations this corresponds to sequences that are about 20 percent identical.
BLOSSUM (Blocks Substitution Matrix)
The BLOSUM matrices, also used for protein database search scoring (the default in blastp), are divided into statistical significance degrees which, in a way, are reminiscent of PAM distances. For example, BLOSUM64 is roughly equivalent to PAM 120. BLOSSUM Blocks Substitution Matrix). BLOSSUM matrices are most sensitive for local alignment of related sequences. The BLOSUM matrices are therefore ideal when tying to identify an unknown nucleotide sequence.