Question: Visualizing Hmm Files Of Hmmer3
1
gravatar for Cjt
4.7 years ago by
Cjt350
Cjt350 wrote:

Is there a way to generate HMM-logos for the outputs of HMMER3? All tools seem to be limited to HMMER2, so neither LogoMat-M nor HMMeditor are working with my .hmm files.

Are there any recommendations how I could easily visualize such files to check the underlying model?

hmm visualization hmmer • 2.0k views
ADD COMMENTlink modified 15 months ago by jockbanan310 • written 4.7 years ago by Cjt350
3
gravatar for Andreas
4.7 years ago by
Andreas2.2k
Singapore
Andreas2.2k wrote:

I don't know of tools for directly visualising HMMs in HMMER2 format. However, you can use hmmconvert to convert the HMMER3 files back to HMMER2 format.

Andreas

ADD COMMENTlink written 4.7 years ago by Andreas2.2k

Somehow I missed this option in the docu. I converted the files and everything works fine! Thank you!

ADD REPLYlink written 4.7 years ago by Cjt350

correct answer, but no upvote? :)

ADD REPLYlink written 4.7 years ago by Andreas2.2k

+1 for a clever but simple solution.

ADD REPLYlink written 4.7 years ago by Casey Bergman16k
2
gravatar for jockbanan
15 months ago by
jockbanan310
Czech Republic
jockbanan310 wrote:

Skylign is now capable of that: 

http://skylign.org/

ADD COMMENTlink written 15 months ago by jockbanan310
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