Opening URLs from Jalview
Both the applet and the desktop application are able to open URLs as 'popups' in your web browser.
Double-clicking on the ID of a sequence will open the first URL that can be generated from its sequence ID. This is often the SRS site, but you can easily configure your own sequence URL links.

Other links for a sequence either derived from any other configured URL links, or imported from the sequence's annotation, are accessed by right clicking to open the sequence pop-up menu, and selecting from the Links submenu.

Configuring URL Links
URL links are defined in the "Connections" tab of the Jalview desktop preferences, or specified as applet parameters.
By default the item "SRS" is added to this link menu. This link will show a web page in your default browser with the selected sequence id as part of the URL.
In the preferences dialog box, click new to add a new link, and edit to modify an existing link, or delete to remove it.
You can name the link, this will be displayed on a new menu item under the "Link" menu when you right click on a sequence id.
The URL string must contain a token that can be replaced with a sequence ID. The simplest token is "$SEQUENCE_ID$", which will be replaced by the chosen sequence id when you click on it.

eg.
UniRef100 = http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$

Links will also be made for any database cross references associated with the sequence where the database name exactly matches a URL link name. In this case, the $SEQUENCE_ID$ string will be replaced with the accession string for the database cross-reference, rather than the sequence ID for the sequence (since Jalview 2.4).

Regular Expression Substitution
A url may contain a string of the form $SEQUENCE_ID=/regular expression/=$. In this case, the regular expression will be applied to the full sequence ID string and the resulting match will be inserted into the URL. Groups of parentheses can be used to specify which regions of the regular expression will be used to generate the URL:

• Each top level parenthesis will yield a URL containing the text matched within that parenthesis.
• Regions matching sub-parentheses within a top-level parenthesis will be concatenated to form the text inserted into the URL for the top-level parenthesis.
Please Note:
• The regular expressions supported by Jalview are those provided by the Stevesoft javaregex package.
• Some characters must be escaped when specifying them as a match within a regular expression.

Many Thanks to Bernd Brandt of the Free University of Amsterdam for testing this new regular-expression expansion feature!