Question: Download Rrna Sequences
0
gravatar for Nicolas Rosewick
5.1 years ago by
Belgium, Brussels
Nicolas Rosewick6.2k wrote:

Hi,

Simple question : Where can I download all rRNA sequences (from human or other species). I found some of them using ensembl biomart but is there maybe other places to find them ?

Thanks

N.

rrna • 15k views
ADD COMMENTlink modified 5.1 years ago by vipin.ts50 • written 5.1 years ago by Nicolas Rosewick6.2k
3
gravatar for Gaik Tamazian
5.1 years ago by
Gaik Tamazian70 wrote:

Take notice of SILVA - a collection of ribosomal RNA databases.

ADD COMMENTlink written 5.1 years ago by Gaik Tamazian70
-1

+1 on the link. Just a head's up on SILVA, it's a great resource (...and I've contributed to the database), but it's skewed toward microbial rRNA and not human. There are many Eukaryotes, but it's not "heavy" in the "human" sequence area.

ADD REPLYlink written 5.1 years ago by Josh Herr5.5k
3
gravatar for vipin.ts
5.1 years ago by
vipin.ts50
New York City
vipin.ts50 wrote:

Go to http://central.biomart.org/ click on Ensembl, Restrict search Gene biotype as rRNA will give the organism specific list of rRNA regions in the genome.

ADD COMMENTlink written 5.1 years ago by vipin.ts50
1
gravatar for Pierre Lindenbaum
5.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum106k wrote:

http://www.ncbi.nlm.nih.gov/nuccore?db=nucleotide&cmd=search&term=rRNA[Feature+key]

Found 5487260 nucleotide sequences.

:-)

ADD COMMENTlink written 5.1 years ago by Pierre Lindenbaum106k

I am not sure this query will be specific enough to return only the rRNA sequenceS. I tried this : (rRNA[Feature key]) AND "Homo sapiens"[porgn:__txid9606] and see the first few results belong to whole chromosomes and not the rRNA sequences.

ADD REPLYlink written 5.1 years ago by Ashutosh Pandey11k

Are you looking at nuclear rRNA, mitochondrial rRNA, or both? Chromosome searching might be time consuming, but can you download all of the Human mitochondrial sequences you can find and parse out all the rRNA operons?

ADD REPLYlink written 5.1 years ago by Josh Herr5.5k
1
gravatar for GAO Yang
5.1 years ago by
GAO Yang250
GAO Yang250 wrote:

Rfam database :a collection of RNA families http://rfam.sanger.ac.uk/

ADD COMMENTlink written 5.1 years ago by GAO Yang250

Which database is better to work? SILVA or RFAM? For human, i found approx 200 sequences Large sub unit LSU+ sample sub unit SUU in SILVA database while in RFAM databases, sequences ranges from 2000-2100.

ADD REPLYlink written 6 months ago by archie40
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