[Jalview-discuss] EMBL-EBI SRS server retirement and sequence identifier links

Hamish McWilliam hpm at ebi.ac.uk
Thu Jan 9 16:13:06 GMT 2014

Hi folks,

By default the JalView provides a link to the the the EMBL-EBI SRS
server in the menu accessed by right-clicking on a sequence identifier.
Since the EMBL-EBI SRS server has been retired (see
http://srs.ebi.ac.uk/srs-retirement.html) users will want to change the
link configuration.

In Desktop JalView this can be done by modifying the "Connections" in
the "Preferences" (see

For the JalView applet this can be done by providing a link
configuration using the 'linkLabel' and 'linkUrl' applet parameters (see

For example to use the "EBI Search" service
(http://www.ebi.ac.uk/ebisearch/) for a link:

A. In Desktop JalView:
- Select "Tools" -> "Preferences..." from the desktop window
- Select the "Connections" tab
- Select the link definition for "SRS" in the "URL link from Sequence ID"
- Click the "Edit" button
- Set the "Link Name" to "Find in EBI Search"
- Set the URL to:
- Click "OK"
- Click "OK"

B. For the JalView applet add the following applet parameters to the
'applet' tag:

<param name="linkLabel_1"    value="Find in EBI Search" />
<param name="linkUrl_1"

All the best,

Mr Hamish McWilliam,
Web Production,
European Bioinformatics Institute (EMBL-EBI),
European Molecular Biology Laboratory,
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SD
United Kingdom

URL: http://www.ebi.ac.uk/

More information about the Jalview-discuss mailing list