NeddyPreddy is a neddylation site predictor that uses SVM to predict neddylation sites from protein sequences.
[NEW] NeddyPreddy web server is available at http://neddypreddy.sabanciuniv.edu (pending publication)
NeddyPreddy uses various python libraries, as well as BLAST+ executables and nr database. If you already have PSSM files of your proteins, you can skip BLAST+ installation.
You can get NeddyPreddy with
git clone https://asyavuz@bitbucket.org/asyavuz/neddypreddy.git
command.
NeddyPreddy is tested on Mac OSX (Yosemite, El Capitan) and Linux (CentOS 5.11, Ubuntu 14.04) systems. If you observe any problems, please report it at the Issues section.
Please refer individual websites of required libraries/tools for their installation instructions.
- BLAST+
- BioPython
- scikit-learn
- IUPred (for local disorder prediction)
- requests (for online disorder prediction)
- BeautifulSoup4 (for online disorder prediction)
The most basic use case would be as following:
python runneddypreddy.py my_protein.fasta
For additional parameters please type:
python runneddypreddy.py --help
NeddyPreddy uses the MIT License (see LICENCE.md). Please open an issue in this page if you have any questions.
If you would like to use NeddyPreddy in your publications, please consider citing:
Yavuz AS, Sozer NB, Sezerman OS. "Prediction of neddylation sites from protein sequences and sequence-derived properties". BMC Bioinformatics, 2015, 16(S18):S9.