This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Download Rrna Sequences

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
• 29,824 views • link
updated by vipin.ts • vipin.ts • written by Nicolas Rosewick Nicolas Rosewick

4 answers

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.

• 0 views • link
written by vipin.ts • vipin.ts

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.

• 1 views • link
written by brianpenghe brianpenghe

The post was deleted.

• 140 views • link
written by User • User

+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.

• 0 views • link
written by Josh Herr Josh Herr

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

Found 5487260 nucleotide sequences.

:-)

• 230 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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.

• 0 views • link
written by Ashutosh Pandey Ashutosh Pandey

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?

• 0 views • link
written by Josh Herr Josh Herr

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

• 0 views • link
written by GAO Yang GAO Yang

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.

• 0 views • link
written by Omics data mining Omics data mining

Log in to answer this question.

More posts like this