consensus sequence

Faye's Avatar


11 Apr, 2014 11:12 PM

How can I find a consensus sequence for family, for either of protein or cds sequences?

  1. 1 Posted by Fabian on 14 Apr, 2014 07:54 AM

    Fabian's Avatar

    Dear Faye,
    thanks for your question.
    I assume by consensus sequence for a family you mean the emitted sequence of a family's HMM. If you want that information, you can just download a family HMM and use "hmmemit" from the HMMer software package to emit a consensus sequence.
    Alternatively, you can download either the protein or CDS alignment and use BioPerl to get the consensus sequence (

    Hope that help.


  2. Fabian closed this discussion on 14 Apr, 2014 07:54 AM.

  3. Faye re-opened this discussion on 16 Apr, 2014 04:12 PM

  4. 2 Posted by Faye on 16 Apr, 2014 04:12 PM

    Faye's Avatar

    Thanks Fabian for your replies,
    It seems like we cannot download your HMM, since when you click on them you get 'Page Not Found' error like :

    And it's not also available in your bulk download pages either

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