413 State Hall, Department of Computer Science, Wayne State University, Detroit MI 48202
Phone: (313) 577-5070 Fax: (313) 577-6868

Link to Dr. Sorin Draghici's home page

 

Onto-Translate Help

Using Onto-Translate

Results

Reading the Results
Analyzing the Results

 

Onto-Translate allows the user to translate easily lists of accession numbers, UniGene clusters and Affymetrix probes into one another.
Using Onto-Translate (top)

 

Once the user is logged in, you will be presented with an HTML form, as shown in Fig. 1. The user will see one of the input form depending on what version she is registered for.

The user is now able to use Onto-Express. The user needs to click on the Onto-Translate icon to use it. Clicking on the Onto-Translate icon gives the following figure.

Figure 1: Onto-Translate Main

The user follows the following steps: 

1. Submits an input file at the text box  "Attach your File:". 

To submit the input file, a user needs to click on "browse" button. Clicking the button opens a file dialog box that displays a list of files on the user's computer. The user selects the input file from the list and click the "Open" button in the dialog box. Then the user selects the name of the organism, which the input list of genes comes from, from the drop down list.

Input File Constraints:
The user needs to submit a list of genes or sequences as a simple ASCII file (file should be prepared in ASCII text editor such as notepad, pico or vi, but not in MS-Word or MS-Excel that creates a binary file). The file can contain either accession numbers, cluster identifiers or probe identifiers but not a combination of them. Each identifier should be listed on a separate line. 

2. Selects the organism from the drop down box  "Select your organism:". 

The user selects the organism by clicking the down arrow of the drop down box. This will open up a dialog box indicating the list of organisms. The user can select a particular organism by right clicking that organism.

3. Select the input format from "Convert From:" radio button. 

The user selects a format Accession Id, Unigene Cluster ID or Affymetrix Probe id by clicking in the radio button besides the name. If the user selects Affymetrix Probe Id then he needs to specify the chip from the drop down box by clicking the down arrow and then selecting the chip and clicking it. The user should provide the file in the same format he/she has selected in this step.

4. Select the target format from "To:" radio button. 

The user selects a format Accession Id, Unigene Cluster ID or Affymetrix Probe id by clicking in the radio button besides the name. If the user selects Affymetrix Probe Id then he needs to specify the chip from the drop down box by clicking the down arrow and then selecting the chip and clicking it.

5. Submits the form by clicking the button.

On clicking the submit button the user can see the result page, if the form has been completed properly or else a suitable error will be displayed.

Figure 2: Onto-Translate Sample Results

 

Results (top)

The results will be shown in a tabular format. The first column represents the input format and the second column represents the target format. 

  Reading the Results (top)

The result is split into number of pages. The user can select the specific page from the drop down box by clicking the down arrow and then clicking on the specific page number. The user needs to press the button to view the results on that page.

Figure 3: Result divided in separate Pages

The user can use the button to get the results emailed to his/her email address.

  Analyzing the Results (top)

The user may want to know more details of a particular sequence for better analysis. The user can ask for more details for each sequence by clicking the hyper linked ID. This will send a request to the server for more details and the server responds with a HTML page that contains Cluster ID, Locus Link, Gene, Gene Title and list of Accession IDs. Each of the identifiers in the page are hyper linked to corresponding section of NCBI. The user can click on these hyperlinks to access particular section of NCBI.


Contact us : Dr. Sorin Draghici   -
               or Purvesh Khatri        -

 

Webmaster - ISBL Team

copyright 2003 Intelligent Systems and Bioinformatics Laboratory, Computer Science Department, Wayne State University