How Scores are given in Substitution matrix like PAM and BLOSUM?

Question

[barathvajramachandran]

hi everyone..

while aligning two protein sequences, amino acid of the query sequence n amino acid of Database sequence is aligned..if both match a score is given..if there is a substitution of aminoacid for eg ( leucine for Isoleucine).how score is given for this alignement?

or simply any one explain how subsitution matrix compares two sequence and align according to the substitution scoring matrix?

[barathvajramachandran]

thank u..I can understand what is substitution matrix..but i couldn't able to understand how log odd scores are given for aminoacid alignment ..can u explain by applying that formula for a small stretch of Sequence..

Answer 1

[Rob]

The Wikipedia page that Istvan links to actually discusses how such matrices are built. You can find a worked example for a very small "block" in my lecture notes on the BLOSUM substitution matrix. Basically, the scores given in BLOSUM are log-odds scores that represent the level to which a particular mutation (aligned amino-acid pair) is observed in a set of conserved "blocks" vs. what you would expect by chance given the abundance of these amino acids.

[Istvan Albert]

That is a really nice set slides on the subject

Answer 2

[Istvan Albert]

There are many resources that describe the concept, for example http://en.wikipedia.org/wiki/Substitution_matrix