BLOSUM62 matrix

Description

A substitution matrix used for sequence alignment of proteins. In LowMACA, it is used to calculate the trident conservation score.

Usage

data("BLOSUM62")

Format

A squared numeric matrix with aminoacids as rownames and colnames

Source

BLOSUM62 from NCBI

Examples

#Load BLOSUM62 and show its structure
data(BLOSUM62)
str(BLOSUM62)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(LowMACA)
Checking if clustalo is in the PATH...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .).
BEGIN failed--compilation aborted.
Warning messages:
1: In .ClustalChecks(ClustalCommand = "clustalo") :
  Clustal Omega is not in the PATH:
You can either change clustalo command using lmParams function or use the web service. See ?setup
2: running command '/usr/bin/perl -MXML::Simple -e 1' had status 2 
3: In .PerlModuleChecks(stop = FALSE, perl = "perl") :
  XML::Simple module for perl is not installed. 
            If you don't want to install a local clustal omega and use the web service, XML::Simple is required

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LowMACA/BLOSUM62.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BLOSUM62
> ### Title: BLOSUM62 matrix
> ### Aliases: BLOSUM62
> ### Keywords: datasets
> 
> ### ** Examples
> 
> #Load BLOSUM62 and show its structure
> data(BLOSUM62)
> str(BLOSUM62)
 int [1:25, 1:25] 4 -1 -2 -2 0 -1 -1 0 -2 -1 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:25] "A" "R" "N" "D" ...
  ..$ : chr [1:25] "A" "R" "N" "D" ...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>