Argo Link Menu

The Argo Link menu provides links to external URLs. Click a command on the Link menu to open a browser window and display a URL, passing properties of the selected feature(s) to that URL. Use the Edit command to add commands to the Link menu. Links that you add are saved between sessions and exported with user preferences.

 Menu Item  Shortcut Active If... Description
Edit always Opens the Edit Feature Links window, which allows you to add items to the Link menu, as described below.
Your Feature Links control numbered function key (number corresponds to link position, first link is F1, second is F2, etc.) selected feature has requisite properties Commands defined in the Edit Feature Links window are included here. Argo provides the NCBI Sequence Viewer command as an example.
Show Smart Domains feature(s) selected Sends the selected feature(s) to the Simple Modular Architecture Research Tool (SMART): an online resource (http://smart.embl.de/) used for protein domain identification and the analysis of protein domain architectures. This link is a special case and does not appear in the Edit Feature Links window.

Edit Feature Links

Click Edit on the Link menu to display the Edit Feature Links window, which allows you to add items to the Link menu. The window contains a row for each user-defined command on the Link menu, plus two blank rows for adding new links:

Edit Feature Links window

Link Name must be unique. This is the name that appears in the Link menu. The Edit Feature Links window lists links alphabetically by link name.

URL Template is the URL that will be displayed when you click this command in the Link menu. Placeholders in the URL template define the properties of the selected feature(s) that will be included in the URL. For example, the URL template for the NCBI Sequence Viewer link is:

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$gi

When you click the NCBI Sequence Viewer command, the $gi placeholder will be replaced by the NCBI Genbank sequence identifier for the feature currently selected in the feature map. For example, if the NCBI Genbank identifier for the selected feature is 27311784, the resulting URL will be:

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=27311784

A URL template can contain zero or more placeholders. A Link command is active only if a selected feature contains the corresponding property for each placeholder. Placeholders begin with a dollar sign ($) and are not case sensitive. The following table lists commonly used placeholders. In addition to the placeholders listed here, any field name on the Properties panel (other than Feature, Location, and Track) can be prefaced with a dollar sign ($) and used as a placeholder.

 Placeholder   Property 
$dna DNA sequence, as shown in the DNA panel of the Inspector.
$mrn mRNA sequence, as shown in the mRNA panel of the Inspector.
$protein Protein sequence, as shown in the Protein panel of the Inspector.
$gi NCBI Genbank identifier for a DNA sequence, as shown in the Feature field of the Properties panel of the Inspector.
For example: ORF3 [GI:289342]
$id Feature identifier, as shown in brackets in the Feature field of the Properties panel of the Inspector.
For example: sc_iso3_15687_17 [2119305921]
$start Starting base number of the feature, as shown in the Location field of the Properties panel of the Inspector.
For example: 100898-127884 (26987)
$stop Ending base number of the feature, as shown in the Location field of the Properties panel of the Inspector.
For example: 100898-127884 (26987)
$length Length of the feature, as shown in the Location field of the Properties panel of the Inspector.
For example: 100898-127884 (26987)
$label Feature label, as shown in the Feature field of the Properties panel of the Inspector.
For example: sc_iso3_15687_17 [2119305921]

Last Updated: Sept 18 2006
Contact: Reinhard Engels
argo-support@broad.mit.edu