Question: Retrieve sequences that generated a HMM profile
0
gravatar for frcamacho
2.5 years ago by
frcamacho190
United States
frcamacho190 wrote:

Hi All,

I have HMM profiles but the raw sequences or multiple sequence alignments are not available. I saw the tool hmmemit, but this randomly generates sequences that match a given profile HMM. I do not want random sequences. Is there a way to obtain sequences or multiple sequence alignment that generated the HMM profile? Additionally, I know skylign generates hmm logos, is there a way to obtain the consensus sequences from the logo? The other option would be to programmatically parse the HMM profile to try to generate the consensus sequence.

Any input would be appreciated!

Thanks in advance.

hmmer • 891 views
ADD COMMENTlink modified 2.5 years ago by Jean-Karim Heriche23k • written 2.5 years ago by frcamacho190
1

hmmemit is your only option as far as I'm aware. It doesn't randomly emit a sequence, it produces the most likely sequence given the hidden states of the Markov Model profile (a kind of consensus sequence).

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Joe17k
2
gravatar for Sej Modha
2.5 years ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

I do not think it is possible to get those sequences as HMM algorithm does not save them, however, you can use hmmemit as you mentioned. It is possible to tweak the hmmemit parameters to match the profile. Please refer to the HMMER documentation.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Sej Modha4.7k
1
gravatar for Jean-Karim Heriche
2.5 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

Unless the original sequences were saved somewhere, you can't get them back from the HMM alone. hmmemit -c will give you a consensus sequence.

ADD COMMENTlink written 2.5 years ago by Jean-Karim Heriche23k
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