I am performing 16S Metagenomic targeted sequencing to profile a mock bacterial community containing 27 bacteria species. My project requires the exact position or loci of the hypervariable regions in each of the bacteria species. I have searched all over the web for a 16S database that shows the loci of hypervariable regions, but haven't been successful. Any help would be much appreciated. I have already looked at: RDP and greengene.
Not I, alas. But I'd dearly like to know myself. So I'm herewith buying into the thread.
I don't know of any database that might give you this information. However, here's a way you might want to go about it:
If you get a 16S hmm, you can get all the regions out of your genomes by running hmmer over them (likely that you will find multiple 16S copies in each genome). Once you extract them all, you can align them to each other and work out where you hyper-variable regions are.
If you're using genomes that are already around, then you can skip the extraction step and just pick the 16S sequences out of greengenes. Though, it's always safer to do it yourself :).
As has already been said - I don't know of any existing reference with this information, and even if there was you might not be able to guarantee that your organisms of interest would be included in it..
Because you're working with a mock community I'm assuming you have the full-length 16S rRNA sequences for your species, or can sequence them easily. A relatively easy way to work out the locations of the hypervariable regions is to use a tool like BLAST or uparse to match primer sequences for each region against the full length sequences from your mock community. Both of these programs give you the alignment positions of the query/target you could easily work out the start/stop position of each hypervariable region.
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