Questions tagged [hmmer]

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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 ...
3
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0answers
39 views

Convert .smp from CDD into HMM file [closed]

Is there a method or tool to convert a .smp file from CDD (Protein Domain File) into a HMM file? I downloaded the CDD files from the FTP site and am more familiar with domain searching with the HMMer ...
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2answers
137 views

Splitting a GenBank file into smaller files

I have a genbank file that I have been trying to run in HMMER using the following command: ...
0
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0answers
80 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 ...
2
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0answers
26 views

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 ...
0
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1answer
98 views

Converting hmmer --tblout to pandas dataframe [closed]

Is there a way to convert a hmmer output to a pandas dataframe? I am also unsure how to load a hmmer tblout table into python via the Bio module. I believe you can call a hmmer format with SeqIO.parse ...
2
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0answers
30 views

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 ...
2
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0answers
44 views

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), ...
2
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1answer
223 views

BUSCO does not find buscos in reference sequence of C. elegans (technical problem)

I am working on a GNU/Linux machine. I have installed BUSCO using conda. I have downloaded the nematode dataset nematoda_odb9.tar.gzhere. I downloaded the reference ...
1
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1answer
120 views

Error compiling HMMER v3.2.1

I tried to compile HMMER v3.2.1 in Cygwin using ./configure followed by make or ...
0
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1answer
1k views

How to uninstall hmmpress from my conda environment?

I have installed hmmpress on my Mac OS X. It is here: which hmmpress /Users/user/anaconda/bin/hmmpress It is available in my ...