Questions tagged [hmmer]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1 vote
2 answers
61 views

How to parse hmmsearch output?

I did hmmsearch with --notextw and --domtblout and I see several results for ids, I want to ...
bobr's user avatar
  • 11
2 votes
1 answer
67 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 ...
donkey's user avatar
  • 163
1 vote
1 answer
88 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 ...
Nok Imchen's user avatar
3 votes
0 answers
88 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 ...
Cody Glickman's user avatar
0 votes
2 answers
519 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: ...
BhushanDhamale's user avatar
0 votes
1 answer
318 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 ...
Cody Glickman's user avatar
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 ...
marilu's user avatar
  • 101
2 votes
0 answers
48 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 ...
marilu's user avatar
  • 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), ...
skc's user avatar
  • 43
2 votes
1 answer
269 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 ...
Biomagician's user avatar
  • 2,459
1 vote
1 answer
222 views

Error compiling HMMER v3.2.1

I tried to compile HMMER v3.2.1 in Cygwin using ./configure followed by make or ...
JernejT's user avatar
  • 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 ...
Biomagician's user avatar
  • 2,459