RESCRIPt full rrna operon RefSeq

[Deni_Ribicic]

Hi folks,

I was wondering is there a possibility to use RESCRIPt to make a custom db containing full rrna operon (both prokaryotic and eukaryotic) from NCBI RefSeq?
Perhaps any other ideas if this is not suitable?

Thanks!

[lizgehret]

Hi @Deni_Ribicic,

Just a quick heads up, I've moved this post into the Community Plugin Support category, since RESCRIPt is not one of the core QIIME 2 plugins. Someone in there should be able to provide some input on this!

Cheers,
Liz

[Nicholas_Bokulich]

Hi @Deni_Ribicic ,
In theory yes you could use RESCRIPt to download all prokaryotic full-length genomes from RefSeq (either with a list of accessions or a query containing the project ID), then trim out the rrna operons. I have not tried, but would be very interested to see what you find!

Here is a paper that did something similar (without RESCRIPt) — and also released a Q2-compatible database. So that might be another option if you want something fast!

[Deni_Ribicic]

Thanks Liz for following up here

[Deni_Ribicic]

Hi @Nicholas_Bokulich,

Thanks for information, specially for highlighted study.

I am not sure I am that well versed to perform suggested trimming, but also finding all accessions or project IDs that would cover most of prokaryotes seems like a tedious work?

I was hoping for some off the shelf solution here, but I see it won't be that easy.

What about eukaryotic rrna operon? This should be also contained in RefSeq?

[Nicholas_Bokulich]

@Deni_Ribicic

I was hoping for some off the shelf solution here, but I see it won't be that easy.

What about eukaryotic rrna operon? This should be also contained in RefSeq?

RefSeq does an enormous amount of the background work (i.e., curating taxonomy and high-quality reference genomes) but they do not have RefSeqs for full rrna operons from any organism... there are "targeted loci" projects where they have already trimmed full SSU, ITS, and LSU rrna from different organisms, but not full operons. This would need to be done by you using the full-length genomes.

@Deni_Ribicic

I am not sure I am that well versed to perform suggested trimming, but also finding all accessions or project IDs that would cover most of prokaryotes seems like a tedious work?

The accessions are already in RefSeq — you download from there, you do not need to identify them on your own. But trimming etc would take some effort... hence why I said "in theory", because RESCRIPt would only help with some of this.

Check out the study I highlighted! That will detail exactly how to do this.