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Visualizing Hmm Files Of Hmmer3

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 hmmer visualization
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updated by Ram Ram • written by Cjt • Cjt

3 answers

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

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written by Andreas Andreas

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

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written by Cjt • Cjt

correct answer, but no upvote? :)

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written by Andreas Andreas

+1 for a clever but simple solution.

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written by Casey Bergman Casey Bergman

Skylign is now capable of that.

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updated by Ram Ram • written by jockbanan jockbanan

There is a visualization script based on LaTeX and TikZ available at https://github.com/lkuchenb/hmmer2pdf that can handle HMMER3 hmm files.

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written by leon.kuchenbecker • leon.kuchenbecker

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