LowMACA relies on three external resources to work properly.
- Clustal Omega version 1.2.x, our trusted aligner (http://www.clustal.org/omega/)
- Ghostscript, a postscript interpreter needed to draw logo plots (http://www.ghostscript.com/)
- Protter, a tool for visualization of proteoforms and annotation of predicted sequences (http://wlab.ethz.ch/protter/start/)
Clustal Omega is a fast aligner that you can download from the link above. Be sure to have clustalo within your PATH.
For Linux and MacOSX users don't forget to run chmod u+x clustalo.
If you don't want to install a local clustalo, you can use the clustal omega web service,
but you will need perl with the modules XML::Simple and LWP. They are generally included in every new perl installation.
Ghostscript is an interpreter of postscript language and that is used by the R library grImport to draw logo plots. It is generally already present in most Unix OS.
- For Linux users, simply download the program from http://ghostscript.com/download/gsdnld.html and compile it
- For MacOS users there is a dmg installer at http://pages.uoregon.edu/koch/
- For Windows users, download the program from http://ghostscript.com/download/gsdnld.html and then you have 3 options:
1. Put C:/Program Files/gs/gs9.05/bin in your PATH once for all (Adjust the path to match your gs installation)
2. Run the command below at every new session of R
# Needed only on Windows - run once per R session
# Adjust the path to match your installation of Ghostscript
> Sys.setenv(R_GSCMD = '"C:/Program Files/gs/gs9.05/bin/gswin32c.exe"')
3. Put the command showed above in your .Renviron file
Protter is a cool predictor and visualizer of protein sequence secondary structures. It's a web-based tool and doesn't require any special setting except from a internet connection.