USAGE:

    In TEDB 1.0 database, we tried to make it more powerful and convenient to be used. The online service and local packages were provided. This USAGE is prepared for the online service of the database. The TEDB 1.0 provide the search option and advance options. (TEDB ID example: TEDB-HS-XXXXX. HS: Homo sapiens; MM: Mus musculus; RN: Rattus norvegicus; O: Others)

1. Search. You can input one or multiple keywords (separated by space character) to search the TEDB database. The search fields including TEDB ID, MHC types, UniProt Accession, Protein Name, Protein Alias, Gene Name, Gene Alias, and Function.

EXAMPLE: Please click on the "Example" button to search "RAN" in Gene Name field. By clicking on the "Submit" button, the related tedb proteins will be shown.

2. Advance Options. Three advance options are provided, including advance search, browse, and BLAST search.

(1) Advance search allows you to input up to three terms to find the information more specifically. The querying fields can be empty if less terms are needed. The three terms could be connected by the following operators:

exclude: If selected, the term following this operator must be not contained in the specified field(s)
and: the term following this operator has to be included in the specified field(s)
or: either the preceding or the following term to this operator should occur in the specified field(s)

EXAMPLE: You can click on the "Example" button to load an instance, which could search human APOB for MHC Class II HLA-DQ8. The human CD95 (TEDB-HS-00001 ) will be shown by clicking on the "Submit" button.

(2) Browse. You can browse the TEDB 1.0 database by species and/or MHC types. With the default setting, you can directly click on the "Submit" button to browse all the proteins.

(3) BLAST search could be used to find the specific protein and/or related homologues by sequence alignment. This search-option will help you to find the querying protein accurately and fast. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined, while the species information could be specified. The default parameters of E-value and species are 0.01 and All species, respectively.

EXAMPLE: You can click on the "Example" button to load the protein sequence of Human Glutamate decarboxylase 1. By clicking on the "Submit" button, you can find the related homologues.

Frequently Asked Questions:

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

A: Please visit the latest version of GPS-MBA 1.0 at http://mba.biocuckoo.org/download.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-MBA 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-MBA 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-MBA 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-MBA 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-MBA 1.0?

A: Please contact the three major authors: Zexian Liu, 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.