Frequently Asked Questions:

1. Q: How to use GPS-Polo 1.0 web service?

A: Please visit the latest version of GPS-Polo 1.0 at http://polo.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-Polo 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-Polo 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-Polo 1.0 could be used directly without any additional packages. Finally, if you can still not view 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: 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-Polo 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-Polo 1.0?

A: Please contact the three major authors: Jun Cao , Dr. Yu Xue and Dr. Jian Ren for details.

 

 

5. 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.

 

 

Supplementary Data (Totally 583KB)

1. Dataset 1 - Prediction results for the phosphoproteomic data. (542KB)

(1) Prediction results of Plk phospho-binding proteins and phosphorylation substrates from experimentally identified phosphorylation sites.
(2) The experimental phosphorylation sites were taken from several major databases, including PhosphoPep, Phospho.ELM, SysPTM, PhosphoSitePlus and HPRD. The literature mining was also carried out to add additional phosphorylation sites. All phosphorylated substrates were mapped to the UniProt database (http://www.uniprot.org/). Five organisms including Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Homo sapiens were considered. Redundant data were cleared.
(3) The experimental phosphorylation sites were submitted to GPS-Polo 1.0 for prediction with the default threshold (Medium). Only phosphorylated serines (S) and threonines (T) were considered for prediction.
(4) Data format. In the head line, the Uniprot ID was sequentially presented following the ">" remark for each proteins; For the sites lines: the 1st column, the position of the predicted site; the 2nd column, the score for the predicted site; the 3rd column, the cutoff for the prediction; the 4th column, the prediction type for the site, predicted to be phosphorylated by Plks (Phosphorylation) or be the phosphor-binding sites of Plks (Phospho-binding); the 4th column, the PSP(7, 7) peptide of the predicted phospho-binding or phosphorylation site. The format could be presented as follows:
>ID
Position Score Cutoff Type Peptide
(5) Created data: May 24, 2011.

2. Dataset 2 - Prediction results of the mitotic-specific Plk-mediated phosphoregulation. (40.7KB)

(1) Prediction results of Plk phospho-binding proteins and phosphorylation substrates which localize at MiCroKit (Centrosome, Midbody, Kinetochore) from experimentally identified phosphorylation sites.
(2) The experimental phosphorylation sites were taken from several major databases, including PhosphoPep, Phospho.ELM, SysPTM, PhosphoSitePlus and HPRD. The literature mining was also carried out to add additional phosphorylation sites. All phosphorylated substrates were mapped to the UniProt database (http://www.uniprot.org/). Five organisms including Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Homo sapiens were considered. Redundant data were cleared.
(3) The experimental phosphorylation sites were submitted to GPS-Polo 1.0 for prediction with the default threshold (Medium). Only phosphorylated serines (S) and threonines (T) were considered for prediction.
(4) Data format. In the head line, the Uniprot ID, gene name, MiCroKit localization information was sequentially presented following the ">" remark for each proteins. For the MiCroKit localization information, "C", "M", "K" was abbreviated from "Centrosome", "Midbody", "Kinetochore"; For the sites lines: the 1st column, the position of the predicted site; the 2nd column, the score for the predicted site; the 3rd column, the cutoff for the prediction; the 4th column, the prediction type for the site, predicted to be phosphorylated by Plks (Phosphorylation) or be the phosphor-binding sites of Plks (Phospho-binding); the 4th column, the PSP(7, 7) peptide of the predicted phospho-binding or phosphorylation site. The format could be presented as follows:
>ID GeneName Localization(C: Centrosome; M: Midbody; K: Kinetochore)
Position Score Cutoff Type Peptide
(5) Created data: May 24, 2011.