RNAs once again work correctly on the NMPDR Development version.
To test the fix,
- Go to the Development Server home page.
- Enter
fig|100226.1.rna.10into the search box. - Select the NMPDR button on the results page to view the feature's data.
In SEED, RNAs are displayed on a special, stripped-down version of the protein page called feature.cgi. This script contains copies of the major protein page subtroutines. Unfortunately, these copies do not use Toby's new framework and don't know anything about Sprout. As a result, the Sprout displays a real protein page, and the protein page itself knows which sections are relevant to the current type of feature and which aren't.
This system broke down for two reasons.
- New code was added to
protein.cgithat automatically terminated the protein page script if a feature wasn't a PEG. - The code in
HTML.pmthat generated the FID link couldn't tell that it was in SPROUT mode because the lucene search page doesn't haveSPROUT=1.
Finally, the genus and species for an RNA feature were not stored in the lucene database. When the lucene search script detects that fact, it will now go directly to the database to rectify the problem.
Comments (2)
Cool. Do I have access to the template on which feature.cgi is returned? The only minor fix needed is that the text of the template says that you are looking at a focus protein encoding gene in green, but in this case, it is an RNA encoding gene.
There is also still the issue that the functional annotation is blank while only the alias column of the context table provides the functional identity--in this case, tRNA-Val.
I believe that Gary Olsen had an idea bout how to make the names of the rnas appear as their functional annotation?
Posted by leslie | October 17, 2006 11:46 AM
Posted on October 17, 2006 11:46
Sprout doesn't use feature.cgi, so the template for RNAs is the same as the template for proteins.
There is a template variable called "protein" that is TRUE for proteins and FALSE for other features. Thus, we can use a to have the template do different things depending on the feature type.
Posted by Bruce | October 18, 2006 8:49 PM
Posted on October 18, 2006 20:49