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THE BLOSUM MATRIX

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What is BLOSUM?

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.

THE APPLICATION OF BLOSUM

THE APPLICATION OF BLOSUM

1. To Be Used in BLAST

used as a scoring matrix when comparing DNA sequences or protein sequences to judge the quality of the alignment. This form of scoring system is utilized by a wide range of alignment software including BLAST.

ADVANTAGES OF BLOSUM

BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences.
Based on local alignments
based on highly conserved stretches of alignments
Higher numbers in the BLOSUM matrix naming denotes higher sequence similarity and smaller evolutionary distance

Example: BLOSUM 80 is used for closely related sequences than BLOSUM 62

BLOSUM vs PAM

BLOSUM

Based on local alignments.
BLOSUM 62 is a matrix calculated from comparisons of sequences with a pairwise identity of no more than 62%.
Based on observed alignments; they are not extrapolated from comparisons of closely related proteins
Larger numbers in matrices naming scheme denote higher sequence similarity and therefore smaller evolutionary distance.

PAM

Based on global alignments of closely related proteins.

PAM1 is the matrix calculated from comparisons of sequences with no more than 1% divergence but corresponds to 99% sequence identity.

Other PAM matrices are extrapolated from PAM1.

Higher numbers in matrices naming scheme denote larger evolutionary distance.

Information theory analysis showed that the matrices are equivalent:
- PAM250 is equivalent to BLOSUM45
- PAM160 is equivalent to BLOSUM62
- PAM120 is equivalent to BLOSUM80

Compared to PAM160 matrix, BLOSUM62 is less tolerant to substitutions involving hydrophilic amino acids and more tolerant to substitutions involving hydrophobic amino acids.

Although both PAM250 and BLOSUM62 detect similarities at the 30% level, since BLOSUM uses such wider range of proteins, PAM250 is actually equivalent to BLOSUM45 when considering all proteins, not just those that are hydrophilic.