SOLpro

Description

SOLpro predicts the propensity of a protein to be soluble upon overexpression in E. coli using a two-stage SVM architecture based on multiple representations of the primary sequence. Each classifier of the first layer takes as input a distinct set of features describing the sequence. A final SVM classifier summarizes the resulting predictions and predicts if the protein is soluble or not as well as the corresponding probability.

License

Download SOLpro (free for academic, non commercial, use)

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of solpro and load default version of solpro as

module avail solpro/ # list available modules
module load solpro   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail solpro

and choose explicit version you want to use. Then run as

predict_sol.sh input output

Documentation

http://scratch.proteomics.ics.uci.edu/explanation.html#SOLpro
http://download.igb.uci.edu/

Homepage

http://scratch.proteomics.ics.uci.edu/explanation.html#SOLpro