Question: How Scores are given in Substitution matrix like PAM and BLOSUM?
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barathvajramachandran0 wrote:

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?

blast alignment • 9.5k views
modified 5.9 years ago by Rob4.1k • written 5.9 years ago by barathvajramachandran0

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..

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Rob4.1k wrote:

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.

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that is  a really nice set slides on the subject

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Istvan Albert ♦♦ 84k wrote:

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