how to retrieve human rRNA annotation

[Xi Wang]

Dear all,

I noticed that there is a comprehensive database on rRNA:

http://www.arb-silva.de/

However, as lack of some biological background knowledge, I failed to get the information for the human. Do anyone know how to retrieve the rRNA annotation of the human genome? Or from some other sources?

Thanks in advance.

Best wishes,
Xi Wang

[lmf_bill]

if my correct understanding, you want to get the list of rRNA in Human. if so, you can get it by using biomart.

[Xi Wang]

Thanks Bill!

Could you please provide more details?

Xi

[lmf_bill]

in biomart:http://www.biomart.org/
first martview-->choose database(ensembl56 sanger UK)--> GRCH37-->fiters-->gene-->gene type-->rRNA
you can get more information from this websit

[Xi Wang]

Thank you very much!

[Katie1]

Looks like the outlook of the Biomart has changed. Could you please provide more detail instructions where and how to donwload the human rRNA sequence!!!

[Xi Wang]

Looks like the outlook of the Biomart has changed. Could you please provide more detail instructions where and how to donwload the human rRNA sequence!!!

I had a quick look through the new version of biomart. Hope the steps below would help.

visit http://central.biomart.org/
Tools / Gene retrieval / Ensembl
1. Select Database (GRCh37.*) ; 2. Restrict Search -> Gene Biotype -> rRNA
Click GO, you will get the list.

[kulukulas]

I had a quick look through the new version of biomart. Hope the steps below would help.

visit http://central.biomart.org/
Tools / Gene retrieval / Ensembl
1. Select Database (GRCh37.*) ; 2. Restrict Search -> Gene Biotype -> rRNA
Click GO, you will get the list.

Hi - it seems to me that this steps will give you only loci of 5S rRNA

Can anybody suggest better source of rRNA sequences? (I need to map my reads against rRNAs and tRNAs to estimate contamination)
Lukasz

[JakobHedegaard]

HI,

Follow this at http://www.arb-silva.de/ to get the human rRNA:
SILVA > Eukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo

Cheers,
Jakob

[kulukulas]

Thanks Jakob!
Very nice database

[neveaire]

I also saw this post (last entry) on finding rRNA and tRNA sequences, which might be helpful. For human hg19 it gave me a list of about 3700 rRNA sequences which I am using with Picard's collectRnaSeqMetrics filter. The BioMart list is about 500, but I haven't investigated the differences.

http://seqanswers.com/forums/archive/index.php/t-12471.html

By the way, I would be interested in hearing rRNA/tRNA contamination rates, particularly after eukaryotic ribodepletion protocols.

[neha]

HI,

Follow this at http://www.arb-silva.de/ to get the human rRNA:
SILVA > Eukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo

Cheers,
Jakob

Hi,

I want to download all human rRNA genes and as suggested by you I have gone through this database but the only confusion I have is it does not report whether it is 5.8S rRNA gene sequence or 18S rRNA gene sequence.

I am concerned whether I will get all rRNA genes or will I miss something.Also are these for latest human genome build that is GRCh37.

Any advice is appreciated.

Thanks
Neha