I am studying three genes common to archaea. But I am looking to find any archaea that are missing any number of these genes. I would like to search as many genomes as I can and as quickly as possible. I was hoping to find a way where I won't have to BLAST each individual organism. Any tips or suggestions for finding these organisms would be great.
1 answer
You could fetch all the predicted proteins of the latest assemblies from ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/archaea//latest_assembly_versions//*_protein.faa.gz
And e.g. screen them against a HMM you build for each of your proteins of interest with HMMER (for some reason their site is down right now).
But really since your db would consist of only a few genes, blasting the available archaeal proteomes against it wouldn't be a big deal..
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