Question

protein profile from alignment

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6.1 years ago

Xylanaser ▴ 80

Hey is there a tool like biopython or cmd program that do profile from protein alignment? And a tool that can comparison profile from db of profiles?

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protein alignment python profile • 1.6k views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 6.1 years ago by Xylanaser ▴ 80

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that do profile from protein alignment

that can comparioson profile from db of profiles

You'll have to explain what you are looking for a bit more in detail.

ADD REPLY • link 6.1 years ago by WouterDeCoster 47k

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I mean - from protein alignment make a profile (somekind ie. freq profiles) I found EMBOSS prophecy. Did someone know something else? And the problem I've got is to find database of well prepered profiles. And program which do comparison of those profiles. could you recommend something?

ADD REPLY • link 6.1 years ago by Xylanaser ▴ 80

score 1 · Answer 1 · 2018-10-27

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6.1 years ago

h.mon 35k

Pfam is a good database of profiles, and HMMER is the program used to create and compare these profiles.

ADD COMMENT • link 6.1 years ago by h.mon 35k

score 1 · Answer 2 · 2018-10-27

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6.1 years ago

fishgolden ▴ 520

HHmake will make hmm profile & hhsearch will compare query profile to db of profiles.

https://github.com/soedinglab/hh-suite

ADD COMMENT • link 6.1 years ago by fishgolden ▴ 520