Utility programs

This section details a number of programs useful for working with structure (VMD), sequence (Seaview) and text (ESS). A brief description of how to obtain additional R packages is also included.

 

Utility programs VMD Seaview ESS Stride Dssp MUSCLE R packages

 

 

VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics. Visit the VMD website for download information and documentation.

Along with the standard documentation you may find my VMD cheat sheet useful. I have also included a link to my .vmdrc file which includes a number of timesaving customizations (see the cheat sheet for full details).

 

 

Seaview

Seaview is a graphical multiple sequence alignment editor. Download information and documentation are available here. I use Seaview to manually check and edit protein sequence alignment files pior to detailed analysis. I believe this should be done with every alignment regardless of how accurate the various automatic tools are supposed to be.

 

 

ESS

Emacs Speaks Statistics (or ESS) is an add-on package for Emacs to allow the easy editting of R scripts. ESS provides a standard interface between a range of statistical programs and statistical processes. It is intended to provide assistance for interactive statistical programming and data analysis, and is based on and extends the capabilities of S-mode. The code is freely available but is not in the public domain. It is distributed under the GNU GPL from here.

 

 

Stride

Stride is a secondary structure analysis program available from the EMBL-Heidelberg. Stride is similar in functionality to the more prevalent dssp (see below). However, stride is much easer to setup as you may be able to simply copy or link to the stride executable distributed within every version of VMD (see above).

 

 

Dssp

Dssp is another secondary structure analysis program available from ... look on google

 

 

MUSCLE

Muscle is a fast multiple sequence alignment program available from the muscle home page. The bio3d 'seqaln()' function currently calls the 'MUSCLE' program, hence MUSCLE MUST BE INSTALLED on your system and in the search path for executables.

 

R packages

There are lots of packages that contain functions to extend the capibilities of R. Most of these add-on packages can be found on CRAN (Comprehensive R Archive Network) which is a network of ftp and web servers around the world that store identical, up-to-date, versions of code and documentation for R. From CRAN you can obtain gzipped tar files named pkg_version.tar.gz, which may in fact be “bundles” containing more than one package.

 

Packages of particular note to the bioinformatics comunity include Seqinr, Bioconductor and Rocr.

To install source packages on your system type

 

$ R CMD INSTALL /path/to/pkg_version.tar.gz

 

to install to the library tree rooted at the first directory given in R_LIBS (see below) if this is set and non-null, and to the default library (the library subdirectory of R_HOME) otherwise.

To find the full path to an installed package (e.g. bio3d) run the following R code :

.find.package("bio3d")

 

To list the contents of a package try this:

ls("package:packagename")

 

substituting packagename for, you guessed it, the package name.

To remove add-on packages

$ R CMD REMOVE packagename