gpcr {bios2mds}

Pre-analyzed G-Protein-Coupled 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 non-redundant sets of non-olfactory class A G-protein-coupled 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 in sub.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 of bios2mds 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 G-protein-coupled 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