Question: How Can I Show Coiled-Coil Predictions In Jalview?
3
gravatar for Michael Kuhn
9.3 years ago by
Michael Kuhn5.0k
EMBL Heidelberg
Michael Kuhn5.0k wrote:

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.)

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ADD COMMENTlink modified 13 months ago by RamRS24k • written 9.3 years ago by Michael Kuhn5.0k
3
gravatar for Fred Fleche
9.3 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

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

ADD COMMENTlink written 9.3 years ago by Fred Fleche4.3k
1

@ 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.

ADD REPLYlink written 9.3 years ago by Fred Fleche4.3k

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?

ADD REPLYlink written 9.3 years ago by Michael Kuhn5.0k

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

ADD REPLYlink written 9.3 years ago by Fred Fleche4.3k
0
gravatar for geoff.barton
5.7 years ago by
geoff.barton10
geoff.barton10 wrote:

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.

ADD COMMENTlink written 5.7 years ago by geoff.barton10
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