Questions tagged [hmmer]

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phmm visualization

I have used HMMER search and I have created a phmm. But I would like to visualize it, not as a logo but as a phmm. I do not have Linux, so I cannot use build hmmer. Is there any web browser that I ...
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phmm blast hmmer

i have created a phmm in hmmer from a multiple alignment focused on E. coli produced in tcoffee from sequences taken from blast similar to my query sequence. I would like to ask how i can compare the ...
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Profile HMM to find sequence motif using Baum-Welch instead of using a given multiple sequence alignment?

I know this can be very problem-specific -- but it seemed to me the standard approach to train an HMM to recognize a binding pattern of a protein is to use the multiple sequence alignment (MSA), ...
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How to quantifiy of specific genes from shotgun metagenome?

I have googled a "lot", couldn't find any specific answer to the question. So, I am here seeking for your guidance. My question is similar to this. I have several metagenome (n=30). But for ...
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58 views

Identify novel protein using Resfam

I am doing a functional metagenomic study. I did the annotation of protein sequences using HMMER against the Resfam database*. The publication is here As a result from the Resfam, I have a list of ...
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Is identity calculated for jackhmmer run locally?

Having trouble finding this, not sure if the -o flag gives us this by default. Sorry if this is a silly question.