Question

Visualizing Hmm Files Of Hmmer3

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12.9 years ago

Cjt ▴ 370

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 • 7.0k views

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 12.9 years ago by Cjt ▴ 370

score 3 · Answer 1 · 2011-05-18

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12.9 years ago

Andreas ★ 2.5k

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 COMMENT • link 12.9 years ago by Andreas ★ 2.5k

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

ADD REPLY • link 12.9 years ago by Cjt ▴ 370

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correct answer, but no upvote? :)

ADD REPLY • link 12.9 years ago by Andreas ★ 2.5k

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+1 for a clever but simple solution.

ADD REPLY • link 12.9 years ago by Casey Bergman 18k

Ram · Answer 2 · 2014-11-10

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9.4 years ago

jockbanan ▴ 420

Skylign is now capable of that.

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.4 years ago by jockbanan ▴ 420

score 0 · Answer 3 · 2019-01-05

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5.3 years ago

leon.kuchenbecker • 0

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

ADD COMMENT • link 5.3 years ago by leon.kuchenbecker • 0