How Can I Show Coiled-Coil Predictions In Jalview?

Question

[Michael Kuhn]

I have an idea on how to hook up a local paircoil2 installation with Jalview through sequence feature files, but I just wanted to check if someone is already aware of an off-the-shelf solution to show for each sequence of an alignment its propensity to form coiled coils. I'm using Jalview right now, but if another program has this, I'd be happy to try it.

(Background: Coiled coils have reduced sequence complexity, and I would like to take that into account when judging alignments.)

Answer 1

[Fred Fleche]

You can give a try to the free version of ICM Browser from MolSoft

[Fred Fleche]

@ Michael Kuhn: Here is the response I got : Thank you also for recommending ICM - unfortunately he would need ICM-Browser-Pro which is $99 for students. ICM cannot predict coiled coils so he would have to annotate the alignment manually.

[Michael Kuhn]

Thanks for the link. I can show the tools panel for the alignment, but the color options (and everything else) is disabled. Perhaps this is a restriction of the free version?

[Fred Fleche]

@ Michael Kuhn: I will check this with a friend of mine who works at Molsoft.

Answer 2

[geoff.barton]

Jalview already does coiled coil predictions via the JPred prediction option. However, if you want to do link to paircoil2 then the lightweight way would be as you suggest via an annotation file. You might also like to post your question on the jalview-discuss mailing list since that will reach the developers as well as other hard core Jalview users.