Question: Retrieve sequences that generated a HMM profile
0
gravatar for camachofrancine
21 months ago by
United States
camachofrancine130 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 • 671 views
ADD COMMENTlink modified 21 months ago by Jean-Karim Heriche21k • written 21 months ago by camachofrancine130
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 21 months ago • written 21 months ago by Joe14k
2
gravatar for Sej Modha
21 months ago by
Sej Modha4.5k
Glasgow, UK
Sej Modha4.5k 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 21 months ago • written 21 months ago by Sej Modha4.5k
1
gravatar for Jean-Karim Heriche
21 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k 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 21 months ago by Jean-Karim Heriche21k
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