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Old 12-02-2011, 08:17 PM   #1
edge
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Default non-coding RNA database

Hi,

Do anybody know any website or ftp link that able to download all the non-coding RNA database of all species?

The link below got non-coding RNA database:
http://research.imb.uq.edu.au/rnadb/default.aspx

Unfortunately, it not allow to download all the non-coding RNA database at the same time.

Thanks for any advice.
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Old 12-03-2011, 01:32 AM   #2
ppgardne
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It'd be nice if that was possible. People often use Rfam for this. However it is not designed to be a complete resource of ncRNA sequences across all species.

There is a proposal to create a resource (RNAcentral) along these lines.
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Old 12-03-2011, 01:39 AM   #3
louis7781x
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miRNA sequences obtained from release of miRBase (release 8.2, July 2006)

It's long time no upadte.
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Old 12-03-2011, 02:07 AM   #4
gringer
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The Silva database is a fairly comprehensive database of non-coding RNA (at least in terms of the most common ncRNA you'll see in RNASeq data):

http://www.arb-silva.de/
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Old 12-03-2011, 07:17 AM   #5
polyatail
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I have found the UCSC mirror at http://www.ncrna.org useful.

Last edited by polyatail; 12-03-2011 at 09:05 AM. Reason: fix broken url
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Old 12-03-2011, 08:00 AM   #6
edge
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Many thanks, ppgardne.
I just download Rfam database.
Silva database suggested by gringer looks quite comprehensive of non-coding RNA sequence
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Old 12-03-2011, 08:02 AM   #7
edge
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Thanks, gringer.
I'm further exploring Silva database to download all non-coding RNA sequence in all species.
Do you got any idea that whether non-coding RNA sequence in Silva database also available and published in NCBI?
Thanks for advice.
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Old 12-03-2011, 08:02 AM   #8
edge
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Hi, polyatail.
It seems like the link http://ncrna.org is broken?
I fail to access it
Thanks.
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Old 12-03-2011, 11:46 AM   #9
gringer
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Just in case it wasn't apparent, Silva is only a rRNA database. I'm not sure how it compares in size to other databases.
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Old 04-01-2012, 09:30 AM   #10
pmiguel
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Default Comparative RNA Web site

Quote:
Originally Posted by gringer View Post
Just in case it wasn't apparent, Silva is only a rRNA database. I'm not sure how it compares in size to other databases.
We were using sequences downloaded from Silva to screen RNAseq data sets for rRNA. Worked pretty well most of the time. However, it turns out that they have very limited animal (including arthropods) mitochondrial rRNAs. As these apparently are sometimes poly adenylated (in oysters, I think), they are potentially a major source of ncRNA in a RNAseq dataset.

Anyway, looks like there is a set of ncRNAs here. It even includes some non-ribosomal ncRNAs. (Mainly tRNAs.) Specifically it does include animal SSU and LSU mitochondrial rRNAs.

--
Phillip
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Old 04-03-2012, 03:54 AM   #11
swaraj
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At this point Biomart is the most comprehensive service to download all non-coding data for multiple organisms. The non-coding RNA are classified into various sub.-categories which have to selected together for each organism.
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