Large (23S/28S, LSU) subunit ribosomal RNA in qiime compatible SILVA database

silva
taxonomy

(Lara Puetz) #1

Dear All,

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?

Many thanks!

Lara


Create data set compatible for qiime 2 in Large subunit ribosomal RNA (28S) SILVA database
(Greg Caporaso) #3

Hi @lara, My understanding is that these are 16S/18S only, and that seems to be confirmed by reviewing the notes file associated with that release. @William or @SoilRotifer, could you confirm this?


(Mike Robeson) #5

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.


(William Walters) #6

Hello Lara,

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.

I hope this helps,
Tony


(Lara Puetz) #7

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?


(Jai Ram Rideout) #8

@lara, did the posts from @SoilRotifer and @William answer your latest question?


(Lara Puetz) #9

@jairideout it did indeed! thank you for all your help @gregcaporaso, @SoilRotifer and @William. I will try to create my own database.


(system) closed #10

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.


(William Walters) #11

Lara, can you tell us if you have created a LSU database? There is another person interested in it if you’re willing to share.


(Matthew Ryan Dillon) opened #12

(victor) #14

Hi!!

I created a part of the LSU database, a 99% clustered and taxonomy at level 10, do you want to take a look of my files?


(William Walters) #15

Hello Victor,

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?


(Afaq) #16

Hi Victor,
I’m going to analyze LSU data using qiime 1. Do you think the database you have will it support qiime 1?
Thanks William for your help


(victor) #17

Hi Afaq,

I’m not sure, I’ve never use qiime 1, but I could send you the files and i hope that help you.

I created the database following the steps in the silva_128_notes, the two files attached were use to create the classifier in qiime2.

let me know if you need something else

LSU_cluster_99


(Afaq) #18

Thanks for the file> Sorry for the delay