Description Usage Format Details Source References Examples
Contains eight amino acid substitution matrices, imported from version 9.1 of the aaindex2 database and PAM matrix calculator of Wageningen Bioinformatics Webportal.
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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.
matrix was produced by "pam" Version 1.0.7
matrix was produced by "pam" Version 1.0.7
matrix was produced by "pam" Version 1.0.7
log odds matrix for 250 PAMs (Dayhoff et al., 1978)
substitution matrix (Henikoff-Henikoff, 1992)
substitution matrix (Henikoff-Henikoff, 1992)
substitution matrix (Henikoff-Henikoff, 1992)
substitution matrix (Henikoff-Henikoff, 1992)
substitution matrix (GONNET et al., 1992)
substitution matrix (Jones et al., 1992)
transmembrane protein exchange matrix (Jones et al., 1994)
substitution matrix built from hydrophobic and transmembrane regions of the Blocks database (Ng et al., 2000)
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.
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.
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Loading required package: amap
Loading required package: e1071
Loading required package: scales
Loading required package: cluster
Loading required package: rgl
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
A R N D C Q E G H I L K M F P S T W Y V
A 6 -6 -3 -3 -6 -3 -2 -1 -6 -4 -5 -6 -4 -7 -1 0 0 -12 -7 -2
R -6 8 -5 -9 -7 -1 -8 -8 -1 -5 -8 1 -3 -8 -3 -2 -5 -1 -9 -7
N -3 -5 7 2 -9 -3 -1 -2 1 -4 -6 0 -7 -8 -5 0 -1 -7 -4 -7
D -3 -9 2 7 -12 -2 3 -3 -3 -6 -11 -4 -9 -13 -7 -3 -4 -13 -10 -7
C -6 -7 -9 -12 9 -12 -12 -8 -7 -5 -13 -12 -12 -11 -7 -2 -7 -14 -3 -5
Q -3 -1 -3 -2 -12 8 2 -6 1 -7 -4 -2 -3 -11 -2 -4 -5 -11 -10 -6
E -2 -8 -1 3 -12 2 7 -3 -4 -5 -8 -4 -6 -12 -5 -4 -5 -15 -8 -6
G -1 -8 -2 -3 -8 -6 -3 6 -8 -9 -9 -6 -7 -8 -5 -1 -5 -13 -12 -5
H -6 -1 1 -3 -7 1 -4 -8 9 -8 -5 -5 -9 -5 -3 -5 -6 -6 -3 -6
I -4 -5 -4 -6 -5 -7 -5 -9 -8 8 -1 -5 0 -2 -7 -6 -2 -12 -5 2
L -5 -8 -6 -11 -13 -4 -8 -9 -5 -1 7 -7 1 -2 -6 -7 -6 -5 -6 -2
K -6 1 0 -4 -12 -2 -4 -6 -5 -5 -7 6 -1 -12 -6 -3 -2 -10 -8 -8
M -4 -3 -7 -9 -12 -3 -6 -7 -9 0 1 -1 11 -3 -7 -5 -3 -11 -10 -1
F -7 -8 -8 -13 -11 -11 -12 -8 -5 -2 -2 -12 -3 9 -9 -6 -8 -4 2 -7
P -1 -3 -5 -7 -7 -2 -5 -5 -3 -7 -6 -6 -7 -9 8 -1 -3 -12 -12 -5
S 0 -2 0 -3 -2 -4 -4 -1 -5 -6 -7 -3 -5 -6 -1 6 1 -4 -6 -5
T 0 -5 -1 -4 -7 -5 -5 -5 -6 -2 -6 -2 -3 -8 -3 1 7 -11 -6 -2
W -12 -1 -7 -13 -14 -11 -15 -13 -6 -12 -5 -10 -11 -4 -12 -4 -11 13 -4 -14
Y -7 -9 -4 -10 -3 -10 -8 -12 -3 -5 -6 -8 -10 2 -12 -6 -6 -4 10 -6
V -2 -7 -7 -7 -5 -6 -6 -5 -6 2 -2 -8 -1 -7 -5 -5 -2 -14 -6 7
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