IFOM-IEO-Campus Istituto Firc di Oncologia Molecolare IFOM-IEO-Campus IEO





NTFootPrinter

.:Tutorial:.







Click Here! to open another window with NTFootPrinter

Give me a Gene...


Input of the gene name First step is choose a gene, the browser is able to take as input:

For this example we use the gene ceh-13. You can try the locus name, or the predicted gene id (R13A5.5).
You can try also to start from the briggsae gene (CBG09160), just select the radio button 'briggsae'.

Now with this button:

This is an icon button

you send the request to genefinder that call MySQL and search for the gene.

Note: this button doesn't work! Is only an example! Use the button into the index.html page



Choose 'Mode' ...


genefinder In the second page (Nematode synteny page), we can verify if the gene exist for elegans and if exist an hortolog in the briggsae genome.
The gene-name is also an hyperlink to a wormbase record that contain complete description of the gene.
To the left we see three buttons to select mode:






.:TEXT MODE:.

offset selection

In the Text mode, you can't execute an interactive selection of the sub-sequences.
You have to select a region BEFORE and AFTER the gene.
Distances are expressed in base pairs (5' and 3' offsets in the image).






.:SLIDER MODE:.


The Java Applet Slider

In this modality you need a Java Virtual Machine installed in your client.
For the interface description and for resolve some problems of browser compatibility try to check the Slider Helper









.:FRAME MODE:.


The Frame Mode

Applet Java and results are in the same html page.
You need a good monitor resolution to take advantages from this modality (1280 x 1024 or more). You can move vericaly the blue frame border in order to hide or show the Slider.
Results are in the bottom frame.




















Get the sequences: THE RESULTS PAGE

The Results Page

Here you can see a screenshoot of the result page:
At the top of the html page there are gene names for the two organism, chromosome and coordinates relatives to chromosome, png images of the offset selected.
'Offset' show the chromosome coordinates of the selected segment of DNA and the length.
The name is directly connected with a record in the database of www.wormbase.org

The Bioinformatic ToolBox contains: - 2 links to sequences in FASTA format (You can copy al the sequence to the clipboard) or save as text file.
- Buttons to send sequences to some tools embedded in this server and external.
Buttons try to open another browser window, so you can keep images and sequences in the result window and make analysis in another window.














Analyze: BIOINFORMATIC TOOLBOX

The Results Page

For a complete description af parameters of the tools and reference consult the specific control panel: