Download Rrna Sequences

Question

[Nicolas Rosewick]

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.

Answer 1

[vipin.ts]

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.

[brianpenghe]

That's indeed the best solution. One thing to add: to download sequences you gotta click on the attribute and select sequence instead of regions.

Answer 2

[User]

The post was deleted.

[Josh Herr]

+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.

Answer 3

[Pierre Lindenbaum]

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

Found 5487260 nucleotide sequences.

:-)

[Ashutosh Pandey]

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.

[Josh Herr]

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?

Answer 4

[GAO Yang]

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

[Omics data mining]

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.