※ Documentation:


Frequently Asked Questions:

1. Q: How to use GPS-SUMO web server?

A: Please visit GPS-SUMO at http://sumosp.biocuckoo.org/down.php. Unlike previous version, the web service does not require a JRE runtime environment. For Windows and Unix/Linux users, please use the keyboard shortcuts "Ctrl+C & Ctrl+V" to copy and paste your FASTA format sequences into TEXT form for prediction. And for Mac users, please use the keyboard shortcuts "Command+C & Command+V". Then please click on the "Submit" button to run the program. The prediction results will be shown in the Prediction form. Again, please click on the ‘Download’ button on the top of the Prediction form to save the results in text or html format.

2. Q: I can't launch the program properly, what should I do?

A: We have tested GPS-SUMO on several operating system, including Windows, Linux and MacOS. For Windows and Linux systems, a latest version of Java Runtime Environment (JRE) package (JAVA 1.6 or later versions) of Sun Microsystems should be pre-installed for using the GPS-SUMO program. Please download and install the proper JRE package on your computer from http://java.com page or our website. However, for Mac OS, the GPS-SUMO could be used directly without any additional packages. Finally, if you still can’t launch the program properly, please send us an email and tell me the OS information on your computer. We will resolve the problem ASAP.

3. Q: Is GPS-SUMO much better than SUMOsp?

A: Yes! Firstly, the fourth-generation GPS (Group-based Prediction System) algorithm was applied in GPS-SUMO. The prediction performance was greatly improved against our previous tools. Secondly, a new feature for SUMO-interaction Motif prediction was added, which will benefit further experimental manipulation. Thirdly, the training data set of GPS-SUMO was updated by searching the scientific literature published before September 2013. Thus, the prediction accuracy of GPS-SUMO was significantly improved. Finally, compared with the former arithmetic, the calculation efficiency of GPS-SUMO has risen greatly. It only cost a few minutes to predict sumoylation sites in human proteome using an average desktop computer.

4. Q: I have 20,000 proteins for prediction, what should I do?

A: For a large-scale prediction, we recommend two approaches for you. You can use the web service but input the sequences for 20 times, with 1,000 proteins per time. Also, please download a stand-alone software of GPS-SUMO linked as below. In the stand-alone versions, the limitation of sequences number is removed. You can use "Batch Predictor" in the local software for a large-scale prediction.

5. Q: There are three thresholds used in your predictor, what do these parameters mean?

A: After GPS-SUMO predictor model was well-trained, we performed an evaluation on this model. From the evaluation, three thresholds with high, medium and low stringencies were chosen for GPS-SUMO. The performance under these three thresholds was presented as follow:

The performance of GPS-SUMO in different threshold
  SUMO Interaction SUMOylation
 
Ac Sn Sp MCC Pr Ac Sn Sp MCC Pr
High 99.36% 52.98% 99.72% 0.5551 58.82% 96.35% 55.34% 98.00% 0.5206 52.61%
Medium 98.84% 78.15% 99.00% 0.5364 37.46% 94.60% 66.84% 95.72% 0.4820 38.51%
Low 97.12% 82.12% 97.24% 0.3818 18.51% 89.49% 76.81% 90.00% 0.3880 23.56%

6. Q: I have a few questions which are not listed above, how can I contact the authors of GPS-SUMO?

A: Please contact the two major authors: Dr. Jian Ren and Dr. Yu Xue for details.

7. Q: I was trying to install the software in Mac OS but my installer says the file is damaged. How can I properly install the software in Mac OS?

A: By default, Mac OS 10.8 or later only allows users to install applications from 'verified sources'. In effect, this means that users are unable to install most applications downloaded from the internet. You can follow the directions below to prevent this error message from appearing.

(1) Open the Preferences. This can be done by either clicking on the System Preferences icon in the Dock or by going to Apple Menu > System Preferences.
(2) Open the Security & Privacy pane by clicking Security & Privacy.
(3) Make sure that the General section of the the Security & Privacy pane is selected. Click the icon labeled Click the lock to prevent further changes.
(4) Enter your username and password into the prompt that appears and click Unlock.
(5) Under the section labeled Allow applications downloaded from, select Anywhere. On the prompt that appears, click Allow From Anywhere.
(6) Exit System Preferences by clicking the red button in the upper left of the window. You should now be able to install applications downloaded from the internet.