How to search CD-HIT clusters against HMM profiles

Question

[siufungstanleyho]

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

[cschu181]

hmmsearch <your.hmm> <your.translated.orfs.fasta>

[siufungstanleyho]

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?

[cschu181]

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.