Similarity Matrix

The following is the similarity score matrix at 250 PAM which is normally used to obtain a rough similarity score or a first alignment. by 2

A similarity matrix is a matrix of scores which express the similarity between two data points. The elements of a similarity matrix measure pairwise similarities of objects - the greater similarity of two objects, the greater the value of the measure. Similarity matrices are used in sequence alignment. Higher scores are given to more-similar characters, and lower or negative scores for dissimilar characters.

http://www.msg.ucsf.edu/local/programs/moloc/smldsc/Image2.gif

http://mendel.ethz.ch:8080/Server/ServerBooklet/_17545_tabular891.gif