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16S ribosomal RNA sequences (Bacteria and Archaea)

NCBI

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#1 lyok

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Posted 14 May 2013 - 11:14 AM

Dear all,

I have a simple question: the NCBI "16S ribosomal RNA sequences (Bacteria and Archaea)" database contains DNA sequences of the 16S RNA gene right?

My confusing start because of the name: 16S ribosomal RNA sequences, but those are not RNA sequences, right?
(since I can use DNA sequences to blast in that database I assume its DNA or the 16S rRNA gene)

or am I missing something here?

Edited by lyok, 14 May 2013 - 11:27 AM.


#2 phage434

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Posted 14 May 2013 - 11:31 AM

Correct. Those are strictly speaking sequences of genes coding for 16S ribosomal RNA.

#3 lyok

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Posted 14 May 2013 - 11:58 AM

Correct. Those are strictly speaking sequences of genes coding for 16S ribosomal RNA.

Ok thanks

Than why do they call it "16S ribosomal RNA sequences", its very confusing and (in my opinion) not correct.

Or are there no RNA databases in general and it is some sort of "unsproken law" that even RNA databases just contain the DNA ?
(for example: Reference RNA sequences (refseq_rna), I am supposing this is also DNA?)

Edited by lyok, 14 May 2013 - 12:02 PM.


#4 phage434

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Posted 14 May 2013 - 01:10 PM

You never actually sequence RNA (well, very rarely, and with great difficulty). You sequence either the DNA which will make the RNA, or you sequence DNA made from the RNA. There are no "real" RNA databases (well, perhaps modified tRNA databases). There are databases of transcripts (created by sequencing DNA made from transcribed RNA). As far as I am aware, no 16S "RNA" databases are made this way. They are all sequences of genomic DNA which will be transcribed into ribosomal RNA. There isn't much difference. It would be great if we really had RNA databases which included the base modifications of the RNA, but that is very difficult.

#5 lyok

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Posted 14 May 2013 - 11:22 PM

You never actually sequence RNA (well, very rarely, and with great difficulty). You sequence either the DNA which will make the RNA, or you sequence DNA made from the RNA. There are no "real" RNA databases (well, perhaps modified tRNA databases). There are databases of transcripts (created by sequencing DNA made from transcribed RNA). As far as I am aware, no 16S "RNA" databases are made this way. They are all sequences of genomic DNA which will be transcribed into ribosomal RNA. There isn't much difference. It would be great if we really had RNA databases which included the base modifications of the RNA, but that is very difficult.

Ok thanks.





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