Home → Questions →

consensus sequence

• Edit

Faye

11 Apr, 2014 11:12 PM

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

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

   

   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 (http://www.bioperl.org/wiki/HOWTO:AlignIO_and_SimpleAlign)

   Hope that help.

   Cheers,
   Fabian

   • Edit

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

   

   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 :
   http://www.treefam.org/family/TF101007/hmm

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

   • Edit