BLOSUM matrix element

The BLOSUM Matrix Element equation computes a matrix element in the i x j substitution matrix used for sequence alignment of proteins. The BLOck SUbstitution Matrix

INPUTS

• `lambda` - a unitless scaling factor
• `p(i,j)` - probability of replacement of a character sequence
• `q(i)` - probability of character i in the the sequence
• `q(j)` - probability of character j in the the sequence

NOTES

In bioinformatics and evolutionary biology, a substitution matrix describes the rate at which one character in a sequence changes to other character states over time. Substitution matrices are usually seen in the context of amino acid or DNA sequence alignments, where the similarity between sequences depends on their divergence time and the substitution rates as represented in the matrix.^[1]

The BLOSUM (BLOcks SUbstitution Matrix)  is used for sequence alignment of proteins. BLOSUM matrices are used to score local alignments between evolutionarily divergent protein sequences.

BLOSUM matrices were first introduced in a paper by Henikoff and Henikoff.^[1] 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.

REFERENCE

[1] Title: Substitution Matrix
Source: Wikipedia
URL: http://en.wikipedia.org/wiki/Substitution_matrix
License: Creative Commons Attribution-ShareAlike 3.0 Unported License

[2] Title: BLOSUM
Source: Wikipedia
URL: http://en.wikipedia.org/wiki/BLOSUM
License: Creative Commons Attribution-ShareAlike 3.0 Unported License