When we consider scoring matrices, we encounter the convention that matrices have numeric indices corresponding to the rows and columns of the matrix. That is, refers to the entry at the first row and the first column. To use this for sequence alignment, we simply associate a numeric value to each letter in the alphabet of the sequence. Thus, one would find the score for a match between A and C at . Since we consider different scoring matrices in this section, we distinguish between them by using different letters for the matrix, refers to the Replacement matrix, to the log odds matric, and so on.
Nucleotide bases fall into two categories depending on the ring structure of the base.
Mutations in DNA are changes in which one base is replaced by another. Since the likelihood of transitions is greater, it is sometimes desireable to create a weight matrix which takes this propensity into account when comparing two DNA sequences. Hydrophobicity matrix Back to Table of Contents . Reconstruct phylogenetic trees and infer ancestral sequences. 71 trees containing 1,572 exchanges were used.