BLAST

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Scoring Matrices

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quency of pairing is 1/500, the odds ratio is 2/1. Converting this to a base 2 loga-

rithm gives a lod score of +1, or 1 bit. Similarly, if the frequency of arginine (R) is 0.1

and its frequency of pairing with L is 1/500, the lod score of an R-L pair is -2.322

bits. In computers, using base e rather than base 2 is more convenient. The values of

+1 and -2.322 bits are 0.6931 and -1.609 nats, respectively.

If you know the direction of change from an evolutionary tree, the pair-wise scores

can be asymmetric. That is, the score of M-L and L-M may not be equal. For sim-

plicity, the direction of evolution is usually ignored, though, and the scores are

symmetrical.

Scoring Matrices

A two-dimensional matrix containing all possible pair-wise amino acid scores is

called a scoring matrix. Scoring matrices are also called substitution matrices because

the scores represent relative rates of evolutionary substitutions. Scoring matrices are

evolution in a nutshell. Take a moment now to peruse the scoring matrix in

Figure 4-2 and compare it to the chemical groupings in Figure 4-1.

Lod scores are real numbers but are usually represented as integers in text files and

computer programs. To retain precision, the scores are generally multiplied by some

scaling factor before converting ...