Frequently Asked Questions:

1. Q: How to use GPS-SNO 2.0 web service?

A: Please visit the latest version of GPS-SNO 1.0 at http://sno.biocuckoo.org/down.php. An JAVA applet will be shown within ten seconds. So, please wait a little while for using the program. 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 use the "Crtl+A & Ctrl+C & Ctrl+V" or "Command+A & Command+C & Command+V" to select, copy and paste the results into a new file, e.g., an Excel file, for further manipulation.

 

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

A: We have tested GPS-SNO 1.0 on several internet browsers, including Internet Explorer 6.0, Netscape Browser 8.1.3 and Firefox 2 under Windows XP Operating System (OS), Mozilla Firefox 1.5 of Fedora Core 6 OS (Linux), and Safari 3.0 of Apple Mac OS X 10.4 (Tiger) and 10.5 (Leopard). For Windows and Linux systems, a latest version of Java Runtime Environment (JRE) package (JAVA 1.4.2 or later versions) of Sun Microsystems should be pre-installed for using the GPS-SNO 1.0 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-SNO 1.0 could be used directly without any additional packages. Finally, if you can still not view the program properly, please send use an email and tell me the OS information on your computer. We will resolve the problem ASAP.

 

3. 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 input the sequences for 20 times, with 1,000 proteins per time. Also, please download a stand-alone software of GPS-SNO 1.0 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.

 

4. Q: I have a few questions which are not listed above, how can I contact the authors of GPS-SNO 1.0?

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

 

5. Q: What I find is the following: If I switch from medium to high threshold, the program eliminates all peptides from Cluster C. This occurs for all the proteins I tried. Perhaps this is something to look at as you optimize the program...(From Dr. Lakshmi Santhanam)?

A: We thanks Dr. Lakshmi Santhanam raised the question. Please try the sequence of P29320, With the high threshold, GPS-SNO can predict its C3 as a potential nitrosylation site. No optimization was made beyond the method that we developed in the manuscript.

6 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.