gpcr {bios2mds}  R Documentation 
Preanalyzed GProteinCoupled Receptor (GPCR) data set
Description
This data set was obtained by the bios2mds
analysis of the two multiple sequence alignment files provided in /msa. The MSA files were prepared as previously described by Deville et al. (2009) and updated with the July 2009 release of Uniprot (http://www.uniprot.org). They correspond to nonredundant sets of nonolfactory class A Gproteincoupled receptors (GPCRs) from H. sapiens and D. melanogaster (283 and 59 sequences, respectively). The data sets from H. sapiens and D. melanogaster constitute the active and supplementary data sets, respectively.
Usage
data(gpcr)
Format
gpcr
is a named list of three elements:
 dif

a named list containing two distance matrices calculated from the
mat.dif
function (distances based on difference scores) with default parameters: sapiens.sapiens
a 283 by 283 matrix of difference scores between the 283 aligned sequences of human GPCRs.
 melanogaster.sapiens
a 59 by 283 matrix of difference scores between the aligned sequences of GPCRs from H. sapiens and D. melanogaster (283 and 59 sequences, respectively)..
 dis

a named list containing sixteen distance matrices calculated from the
mat.dis
function (distances based on dissimilarity scores) for the eight substitution matrices insub.mat
(other parameters by default): sapiens.sapiens$*
are 283 by 283 matrices of dissimilarity scores between the 283 aligned sequences of human GPCRs.
 sapiens.sapiens$PAM40
is calculated with PAM40.
 sapiens.sapiens$PAM80
is calculated with PAM80.
 sapiens.sapiens$PAM120
is calculated with PAM120.
 sapiens.sapiens$PAM250
is calculated with PAM250.
 sapiens.sapiens$BLOSUM30
is calculated with BLOSUM30.
 sapiens.sapiens$BLOSUM45
is calculated with BLOSUM45.
 sapiens.sapiens$BLOSUM62
is calculated with BLOSUM62.
 sapiens.sapiens$BLOSUM80
is calculated with BLOSUM80.
 sapiens.sapiens$GONNET
is calculated with GONNET.
 sapiens.sapiens$JTT
is calculated with JTT.
 sapiens.sapiens$JTT_TM
is calculated with JTT_TM.
 sapiens.sapiens$PHAT
is calculated with PHAT.
 melanogaster.sapiens$*
are 59 by 283 matrices of dissimilarity scores between the 283 aligned sequences from H. sapiens and D. melanogaster
 melanogaster.sapiens$PAM40
is calculated with PAM40.
 melanogaster.sapiens$PAM80
is calculated with PAM80.
 melanogaster.sapiens$PAM120
is calculated with PAM120.
 melanogaster.sapiens$PAM250
is calculated with PAM250.
 melanogaster.sapiens$BLOSUM30
is calculated with BLOSUM30.
 melanogaster.sapiens$BLOSUM45
is calculated with BLOSUM45.
 melanogaster.sapiens$BLOSUM62
is calculated with BLOSUM62.
 melanogaster.sapiens$BLOSUM80
is calculated with BLOSUM80.
 melanogaster.sapiens$GONNET
is calculated with GONNET.
 melanogaster.sapiens$JTT
is calculated with JTT.
 melanogaster.sapiens$JTT_TM
is calculated with JTT_TM.
 melanogaster.sapiens$PHAT
is calculated with PHAT.
 mmds

a typical example of metric MDS analysis with the
mmds
function ofbios2mds
using GPCRs from H. sapiens as active data and GPCRs from D. melanogaster, N. vectensis and C. intestinalis for supplementary data. sapiens.active
metric MDS analysis of active data from H. sapiens.
 melanogaster.project
projection of supplementary data from D. melanogaster onto the human active space.
 vectensis.project
projection of supplementary data from N. vectensis onto active the human space.
 intestinalis.project
projection of supplementary data from C. intestinalis onto the human active space.
Source
Deville J, Rey J and Chabbert M (2009) An indel in transmembrane helix 2 helps to trace the molecular evolution of class A Gproteincoupled receptors. J Mol Evol 68: 475 489.
Examples
# loading gpcr
data(gpcr)
# displaying the matrix of differences scores between GPCRs sequences
# from H. sapiens
gpcr$dif$sapiens.sapiens
# displaying the matrix of dissimilarity scores between GPCRs sequences
# from H. sapiens
gpcr$dis$sapiens.sapiens$PAM250
# displaying the matrix of dissimilarity scores between GPCRs sequences
# from H. sapiens and D. Melanogaster calculated with the BLOSUM45 matrix
gpcr$dis$melanogaster.sapiens$BLOSUM45
# displaying mmds analysis of the MSA of GPCRs from H. sapiens
# and D. Melanogaster
gpcr$mmds$sapiens.active
gpcr$mmds$melanogaster.project