I am curious to know if the SILVA 128 QIIME compatible database includes the large (23S/28S, LSU) subunit ribosomal RNA reference sequences or does it only contain the reference sequences for small (16S/18S, SSU)16S/18S?
Hi @gregcaporaso and @lara . Yes, these files only contain the 16S/18S rRNA sequences (i.e. SSU only), as they are phylogenetically related genes, i.e. can be aligned to one another. The LSU genes differ.
However you can follow the simple approach here to make your own LSU database. This is what I've generally done to start making make my 23S databases. Although @William may have more details to add to this.
The QIIME-compatible SILVA 128 database only contains SSU data. I haven't tried to construct a similar database using the LSU data from SILVA.
The taxonomy strings in the LSU sequences appear to be in the same format as the SSU data, so you may be able to build a new database following the instructions in the SSU information file.
Hi @gregcaporaso,
Thank you for your reply. I suspected the same but thought I'd ask. Do you know how intuitive it is to include or create a qiime compatible version of the whole SILVA database which will include the 23S/28S, LSU rRNA sequences?
I personally didn't have LSU data to use, but another user, @amm59063 (Afaq) is in need of the LSU database. Is there any way you could share it with Afaq?