How can I find a consensus sequence for family, for either of
protein or cds sequences?
|?||Show this help|
|ESC||Blurs the current field|
|r||Focus the comment reply box|
|^ + ↩||Submit the comment|
You can use
Command ⌘ instead of
Control ^ on Mac
1 Posted by Fabian on 14 Apr, 2014 07:54 AM
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.
Fabian closed this discussion on 14 Apr, 2014 07:54 AM.
Faye re-opened this discussion on 16 Apr, 2014 04:12 PM
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 :
And it's not also available in your bulk download pages either