Question: Where Do I Find The 16S Rdna Reference Sequences (Metagenomics)
7
gravatar for datablaze
7.1 years ago by
datablaze80
datablaze80 wrote:

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!

rrna metagenomics database • 20k views
ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 7.1 years ago by datablaze80
9
gravatar for Michael Barton
7.1 years ago by
Michael Barton1.8k
Akron, Ohio, United States
Michael Barton1.8k wrote:

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.

ADD COMMENTlink modified 6.9 years ago • written 7.1 years ago by Michael Barton1.8k

I believe the alignment tool on GreenGenes is out of service

ADD REPLYlink written 2.8 years ago by jolespin90
4
gravatar for lexnederbragt
7.1 years ago by
lexnederbragt1.2k
Oslo, Norway
lexnederbragt1.2k wrote:

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

ADD COMMENTlink written 7.1 years ago by lexnederbragt1.2k
1

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

ADD REPLYlink written 7.1 years ago by datablaze80
1

+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.

ADD REPLYlink written 6.9 years ago by Michael Barton1.8k
3
gravatar for Yvan
6.8 years ago by
Yvan30
CBU, Bergen, Norway
Yvan30 wrote:

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

ADD COMMENTlink modified 4.2 years ago by Eric Normandeau9.5k • written 6.8 years ago by Yvan30
2
gravatar for Pierre Lindenbaum
7.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum98k wrote:

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/

ADD COMMENTlink written 7.1 years ago by Pierre Lindenbaum98k
6

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

ADD REPLYlink written 7.1 years ago by Brad Chapman9.1k

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.

ADD REPLYlink written 7.1 years ago by datablaze80

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

ADD REPLYlink written 7.1 years ago by datablaze80
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