1. Q: How to use SUMOsp 2.0 web server?

A: Please visit the latest version of SUMOsp 2.0 at http://bioinformatics.lcd-ustc.org/sumosp/prediction.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.

A: We have tested SUMOsp 2.0 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 SUMOsp 2.0 program. Please download and install the proper JRE package on your computer from "Java(TM) SE Runtime Environment 6 Update 3" page or our website. However, for Mac OS, the SUMOsp 2.0 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: Is SUMOsp 2.0 much better than SUMOsp 1.0?

A: Yes! Firstly, we reivsed our previous GPS (Group-based Phosphorylation Scoring) algorithm for SUMOsp 2.0. The Accuracy of SUMOsp 2.0 was considerably improved against SUMOsp 1.0. Also, in SUMOsp 1.0, it's a heavy burden if too many sequences are submitted. Usually, SUMOsp 1.0 only permit less than 20 sequences per time. However, SUMOsp 2.0 will use the local CPU for computation. Thus, an up to 1,000 proteins (average length ~1000aa) could be input. Finally, the speed of SUMOsp was greatly improved. Even in our laptop (IBM ThinkPad R51, 1.60GHz, 768MB), it only cost <3 minutes to predict sumoylation sites for 1,000 protein sequences (average length ~1,000aa).

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 input the sequences for 20 times, with 1,000 proteins per time. Also, please download a stand-alone software of SUMOsp 2.0 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.

5. Q: I have a few questions which are not listed above, how can I contact the authors of SUMOsp 2.0?

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

Comparisons of SUMOsp 2.0 with SUMOplot and SUMOsp 1.0

We searched the PubMed with keywords of “SUMO” and “sumoylation”, and manually collected 355 experimentally verified sumoylation sites in 212 proteins, which were published before Oct. 18th, 2007. After redundant clearing, we arbitrarily took the 279 sumoylation sites from 166 proteins published before Feb, 2007 as the training data set. And the remnant 53 sites in 31 proteins were not included in training as an additional data set for performance evaluation. We compared SUMOsp 2.0 to SUMOplot and SUMOsp 1.0, with both the training data and the new data.