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Mmseqs profiles for speed up #11

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SilasK opened this issue May 17, 2020 · 3 comments
Open

Mmseqs profiles for speed up #11

SilasK opened this issue May 17, 2020 · 3 comments

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@SilasK
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SilasK commented May 17, 2020

Dear @takaram Do you think it would be possible to make a mmseqs2 implementation of kofam_scan. mmseqs2 profiles work analogous to hmmer profiles but should be 300 times faster.

I can help with the implementation.

What do you think?
@cmkobel
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cmkobel commented Jun 8, 2023

Did anyone implement this in a fork? Or does anyone have a script that works analogously to kofam_scan?

@SilasK
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SilasK commented Jun 8, 2023

No response from the developer since three years is probably to be interpreted as a No.

@SilasK
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SilasK commented Jun 8, 2023

We would need the original alignments, that's all..

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@cmkobel @SilasK