sub.mat {bios2mds}

Amino acid substitution matrices

Description

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)

Source

The matrices were downloaded from the AAindex database at http://www.genome.jp/aaindex or were calculated on the PAM server at http://www.bioinformatics.nl/tools/pam.html.

References

Kawashima S and Kanehisa M (2000) AAindex: amino acid index database. Nucleic Acids Res 28:374.

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 A 89:10915-9.

Jones DT, Taylor WR and Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl. Biosci 8:275-282.

Jones DT, Taylor WR and Thornton JM (1994) A mutation data matrix for transmembrane proteins. FEBS Lett 339:269-75.

Ng PC, Henikoff JG and Henikoff S (2000) PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Bioinformatics 16:760-6.

Gonnet GH, Cohen MA and Benner SA (1992) Exhaustive matching of the entire protein sequence database. Science 256:1443-1445.

Examples

# loading
data(sub.mat)

# displaying PAM40:
sub.mat$PAM40