Contains eight amino acid substitution matrices, imported from version 9.1 of the aaindex2 database
and PAM matrix calculator of Wageningen Bioinformatics Webportal.
Usage
data(sub.mat)
Format
A named list with eight elements corresponding to a 20 by 20 named matrix. Rows and columns names
correspond to the twenty strict amino acids.
Details
PAM40
matrix was produced by "pam" Version 1.0.7
PAM120
matrix was produced by "pam" Version 1.0.7
PAM160
matrix was produced by "pam" Version 1.0.7
PAM250
log odds matrix for 250 PAMs (Dayhoff et al., 1978)
BLOSUM30
substitution matrix (Henikoff-Henikoff, 1992)
BLOSUM45
substitution matrix (Henikoff-Henikoff, 1992)
BLOSUM62
substitution matrix (Henikoff-Henikoff, 1992)
BLOSUM80
substitution matrix (Henikoff-Henikoff, 1992)
GONNET
substitution matrix (GONNET et al., 1992)
JTT
substitution matrix (Jones et al., 1992)
JTT_TM
transmembrane protein exchange matrix (Jones et al., 1994)
PHAT
substitution matrix built from hydrophobic and transmembrane regions of the Blocks database (Ng et al., 2000)
Kawashima S and Kanehisa M (2000) AAindex: amino acid index
database. Nucleic Acids Res28:374.
Dayhoff MO, Schwartz R and Orcutt BC (1978) A model of Evolutionary Change in Proteins.
Atlas of protein sequence and structure (volume 5, supplement 3 ed.). Nat. Biomed. Res. Found.. pp. 345-358.
Henikoff S and Henikoff JG (1992) Amino acid substitution matrices from protein blocks.
Proc Natl Acad Sci U S A89:10915-9.
Jones DT, Taylor WR and Thornton JM (1992) The rapid generation of mutation data matrices
from protein sequences. Comput Appl. Biosci8:275-282.
Jones DT, Taylor WR and Thornton JM (1994) A mutation data matrix for transmembrane
proteins. FEBS Lett339:269-75.
Ng PC, Henikoff JG and Henikoff S (2000) PHAT: a transmembrane-specific substitution
matrix. Predicted hydrophobic and transmembrane. Bioinformatics16:760-6.
Gonnet GH, Cohen MA and Benner SA (1992) Exhaustive matching of the entire protein sequence database.
Science256:1443-1445.