Abstract
An amino acid index, which is a set of 20 numerical values, represents the various properties of amino acids. A similarity matrix, also called a mutation matrix, which is a set of 20×20 numerical values, represents the similarity between amino acids, and is used for protein sequence alignments and similarity searches. We have collected 402 amino acid indices and 42 published mutation matrices, and organized the database named AAindex which is made publicly available on the Internet.
