Where Do I Find The 16S Rdna Reference Sequences (Metagenomics)

Question

[datablaze]

I have 454 based metagenomic sequencing (rRNA) reads that I was asked to blast against bacterial 16S rDNA. So far I was unable to find a data source (fasta file) that would have only these sequences for all known, sequenced organisms.

Does anyone know a good source for it? Also I would appreciate a link to a good introductory paper on the methodology. I found a bunch of papers based on 16S data but most skip the essential part of how to actually do the mapping and what problems/challenges should I be looking out for.

Thanks a lot for your help!

Answer 1

[Michael Barton]

Try GreenGenes it's a 16S rRNA database with a lot of tools. You can also download their reference alignment which you can use as a template alignment for your own genes. In analysing 16S I would try looking at mothur which is very useful for analysing 16S data, there are many analysis examples on the mothur wiki. It's a command line tool but it's relatively straightforward to pick up.

EDIT: Try looking at silva too which also contains alignments of 16S sequences

EDIT:Also checkout QIIME (pronounced chime) mentioned below which is excellent as an analysis pipeline for 16S data produced by 454.

[jolespin]

I believe the alignment tool on GreenGenes is out of service

Answer 2

[lexnederbragt]

Besides the actual mapping and database(s) for that, you might want to consider denoising your data. Check out http://qiime.sourceforge.net/ for pyronoise, or this paper that just came out: http://www.ncbi.nlm.nih.gov/pubmed/20805793

[datablaze]

Thank, very helpful, I'll look at these resources.

[Michael Barton]

+1 for QIIME. I've had a look at this tool recently and it's capable of end to end analysis of 16S sequences produced by 454.

Answer 3

[Yvan]

Hello, You can use the Silva/ARB database/server http://www.arb-silva.de/ Good luck yvan

Answer 4

[Pierre Lindenbaum]

If found 327174 entries using the simple query ("16S rRNA" OR "16S ribospmal rRNA") using GenBank: http://www.ncbi.nlm.nih.gov/nuccore

Another useful resource could be the RDP database for pyrosequencing : http://pyro.cme.msu.edu/

[Brad Chapman]

The resource page at: http://rdp.cme.msu.edu/misc/resources.jsp has downloads. The file you are looking for is likely: http://rdp.cme.msu.edu/download/release10_22_unaligned.fa.gz

[datablaze]

Thanks for the answer. Some issues I have is that getting 300K sequences via the web interface (or web API for that matter) at NCBI does not seem to be feasible plus the search term seems to be too broad. I do know of RDP but I spent more than an hour there and I was unable to find the data.

[datablaze]

Thanks a lot.I have been on that page but with so many links there I haven't noticed that.