Questions tagged [hmmer]
The hmmer tag has no usage guidance.
11
questions
2
votes
1
answer
63
views
How to determine the phylogeny of a specific set of genes
My goal is to understand the phylogeny of genes involved in bacterial restriction-modification systems, in psychrophilic bacteria.
To do so here is what I have done.
Downloaded the protein sequences ...
- 163
1
vote
1
answer
76
views
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 ...
- 111
3
votes
0
answers
83
views
Convert .smp downloaded from NCBI CDD into HMM(.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 ...
- 173
0
votes
2
answers
476
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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:
...
- 101
0
votes
1
answer
285
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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 ...
- 173
2
votes
0
answers
35
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 ...
- 101
2
votes
0
answers
46
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 ...
- 101
2
votes
0
answers
47
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), ...
- 43
2
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1
answer
264
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 ...
- 2,459
1
vote
1
answer
202
views
Error compiling HMMER v3.2.1
I tried to compile HMMER v3.2.1 in Cygwin using
./configure
followed by
make
or
...
- 11
1
vote
1
answer
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 ...
- 2,459