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Command line NoD predictor

Download: clinod v1.3 (0.5Mb) (old version)

The command line NoD predictor is a Java application which can be run on any platform that supports Java 6. The NoD predictor requires the SNNS Batch Interpreter V 1.0 executable which is a part of the Stuttgart Neural Network Simulator (SNNS) v 4.2 software suite. Please note that JPred secondary structure predictions are not currently available for the NoD command line predictor. For more details on how to run the predictor consult the command line predictor help pages.

NoD local server

Download: NoD virtual appliance download (1Gb)

For ease of installation on Windows, Mac and Linux, the NoD virtual appliance is a complete installation of the NoD server. The appliance comes fully configured to run the NoD server. To run the appliance you must first install the freely available VMWare Player or Oracle VirtualBox virtualization environments. We have tested the NoD appliance with VMWare Player on Windows and Linux, and VirtualBox on Windows, Linux and Mac. However, you are not limited to these virtualization systems and can use the NoD appliance with any other virtualization platform. For more information on how to use this virtual appliance please refer to the Virtual Appliance installation help pages.
Please note that JPred secondary structure predictions are not currently available from the NoD virtual appliance. However, we are working on it for a future release.

Datasets Currently Available For Download

Download: All human predicted NoLSs with Uniprot or RefSeq accessions (1Mb)

The fields (columns) of the dataset are as follows:

  1. IPI protein accession
  2. Uniprot identifiers mapped to the IPI accession, separated by semicolons
  3. Refseq identifiers mapped to the IPI accession, separated by semicolons
  4. Start position of the predicted NoLS within the protein sequence
  5. End position of the predicted NoLS within the protein sequence
  6. Sequence of the predicted NoLS
The character "\t" is used to separate each column.

Some proteins are predicted to harbour more than one NoLS.

Source Code Download

NoD is an open source project so you are welcome to download and use it free of charge. NoD is licenced under the Apache 2 licence. NoD source code and the web site in Eclipse project is available for download as well as the NoD predictions for the human proteom as MySQL database dump.