Search genomes for hits from protein HMM

Question

[Gio]

Hello all,

My goal is to build a phylogenetic tree of a selected set of genomes based on proteins solely related to RM systems.

Thus I have aligned all of my RM system proteins. Selected the relevant genomes. Built an HMM from the RM protein sequences using HMMER3.

I now need to search the genomes (DNA sequences in FASTA format) using this HMM built from proteins.

However HMMER doesn't seem to have a search function across alphabets (DNA/AA). How can this be accomplished? Do I have to translate my >200 genomes into proteins using a program that finds and translates ORF? Any recommendations for such a program?

Thank you

Answer 1

[Mensur Dlakic]

Yes, you will have to do gene finding first.

https://github.com/hyattpd/Prodigal

prodigal -i genome.fa -a proteome.faa -o /dev/null -q