Difference between revisions of "Profppikernel"

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The .tar.gz source package contains all source codes together with a sample classification problem. Download it [http://www.rostlab.org/~hampt/profppikernel/profppikernel-1.0.1.tar.gz here] and compile and install it with the included make based installation (see the included README file). The main executable is '''profppikernel'''.
 
The .tar.gz source package contains all source codes together with a sample classification problem. Download it [http://www.rostlab.org/~hampt/profppikernel/profppikernel-1.0.1.tar.gz here] and compile and install it with the included make based installation (see the included README file). The main executable is '''profppikernel'''.
   
Alternatively, you can try the precompiled version (available [http://www.rostlab.org/~hampt/profppikernel/profppikernel-1.0.1.precomp.tar.gz here]). See the README file for installation instructions.
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Alternatively, you can try the precompiled version (available [http://www.rostlab.org/~hampt/profppikernel/profppikernel-1.0.1.precomp.tar.gz here]). Again, eee the README file for installation instructions.
   
 
== Best human predictions ==
 
== Best human predictions ==

Revision as of 04:27, 31 December 2014

Description

Profppikernel uses an accelerated version of the original profile kernel [1] to train SVM based protein-protein interaction (PPI) prediction models and to predict new PPIs from sequence alone.

In the first mode of operation, 'training', the user provides evolutionary protein profiles and PPIs between them (labels) as input and profppikernel outputs a folder with all model files required for predictions. In the second mode, 'prediction', the user provides the path to such a model folder and to the query profiles and PPIs. profppikernel then predicts their probability to interact.

Availability

The .tar.gz source package contains all source codes together with a sample classification problem. Download it here and compile and install it with the included make based installation (see the included README file). The main executable is profppikernel.

Alternatively, you can try the precompiled version (available here). Again, eee the README file for installation instructions.

Best human predictions

We have predicted all protein pairs in human for which both (C3) or one (C2) protein are sequence-dissimilar to known reliably annotated human interactions. The best 100,000 predictions in either class can be downloaded here.

Bugs and Other Issues

Please report bugs and other issues via Bugzilla.

Reference

T. Hamp, T. Goldberg and Rost, B. (2013): Accelerating the Original Profile Kernel. PLoS One, 8(4), e68459

Contact

For questions, please contact hampt@rostlab.org