Hi Paolo - just cc'ing the dev list so we all have a record of the emails! On 30/03/2012 10:35, Paolo Di Tommaso wrote: > > T-Coffee can produce the alignment score in a text file, like this > > http://tcoffee.crg.cat/data/79609a4a/sh3.score_ascii OK. > > Merging this information with the resulting sequence alignment, should > not be too difficult to visualize the resulting color scheme in Jalview. yes. > > In my opinion there are two main use cases: > > 1) The users (or the developer in the case of the applet) provide the > sequences alignment and the score ascii files as produced by T-Coffee. > Jalview manage to convert the scores in its internal structures and > render the alignment using the associated color scheme. > > > 2) The user submits a T-Coffee alignment request. The web service send > back the score ascii other than the alignment fasta file, and then the > case fallback to the previous one. > > > At the beginning I would focus on the most simple scenario (which by > accident is the one on which I'm more interested :)), I mean the > Jalview applet version and make it able to render the colored T-Coffee > alignment, adding an extra parameter to specify the generated > score_ascii to the applet. > > > What do you think about that? I think it sounds great. The TCoffee scores fall into a similar class as JNet scores - which get turned into alignment annotation and can be specified separately to the alignment. Extending the web service will require a bit more familiarity with Jalview's code, so I'd definitely suggest #1 is the place to start.
Jim. _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
