Question: How to search CD-HIT clusters against HMM profiles
0
gravatar for siufungstanleyho
14 months ago by
siufungstanleyho0 wrote:

Hi there,

I have a metagenome assembly with ORFs predicted with prodigal and clustered with CD-HIT - resulting in a file with clusters of fasta headers and a normal unsorted fasta file.

I would like to search this against the pVOGs database (http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads.html). I've downloaded the pVOGS HMM profiles and tried to work out how to search against it but I can't make sense of the HMMER manual. I am doing this so I can filter out any contigs that doesn't have hits (or the hits are really sparse).

Thanks for helping in advance

assembly gene • 303 views
ADD COMMENTlink written 14 months ago by siufungstanleyho0
1
hmmsearch <your.hmm> <your.translated.orfs.fasta>
ADD REPLYlink modified 14 months ago • written 14 months ago by cschu1812.5k

Thanks for your reply, How do I do this if the pVOGs db is made up of 100s of hmm profiles and my clustered genes are in an unsorted fasta file and cluster headers are in another file?

ADD REPLYlink written 14 months ago by siufungstanleyho0
1
  1. I think you can just cat the .hmm files together into one big one. Alternatively, run a loop over all .hmm files (but I don't think it's necessary).
  2. This unsorted fasta file is one of the outputs of CD-HIT, isn't it? In this case, you should have your cluster representatives in that file.
ADD REPLYlink written 14 months ago by cschu1812.5k
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