Question: Finding Rrna Genes In Metagenomic Data
11
gravatar for toshnam
8.7 years ago by
toshnam620
Seoul, Republic of Korea
toshnam620 wrote:

Hi all,

I have 454 based metagenomic reads. I want to search for all ribosomal RNA in it is.
So I need a rRNA database for searching rRNA in my sequences using BLAST.
Can anybody recommend a good rRNA database that is not aligned format but just FastA format?

Also, if you have good method for rRNA prediction of metagenomic reads, please tell me about it.

Thank you for your reply in advance.

rrna metagenomics rna database • 8.2k views
ADD COMMENTlink modified 4.2 years ago by k09im010 • written 8.7 years ago by toshnam620
3

see previous question "Where do I find the 16S rDNA reference sequences (metagenomics)" http://biostar.stackexchange.com/questions/2318

ADD REPLYlink written 8.7 years ago by Pierre Lindenbaum120k

Oh didn't see this. Some good answers there including green genes :)

ADD REPLYlink written 8.7 years ago by Treylathe940
9
gravatar for Treylathe
8.7 years ago by
Treylathe940
San Francisco
Treylathe940 wrote:

Here're are a few.

Green genes has 16s rRNA http://greengenes.lbl.gov/ Silva is an rRNA database you can blast http://www.arb-silva.de/

As for the second part of the question, I haven't used it but this paper describes a method to do that that was recommended to me. Someone else here might have a better way. http://bioinformatics.oxfordjournals.org/content/25/10/1338.full

ADD COMMENTlink modified 6.9 years ago by Michael Dondrup46k • written 8.7 years ago by Treylathe940

The method Trey refers to is Meta-RNA: http://weizhong-lab.ucsd.edu/meta_rna/

ADD REPLYlink modified 6.9 years ago by Michael Dondrup46k • written 8.4 years ago by Casey Bergman18k
2
gravatar for Prohan
8.7 years ago by
Prohan350
United States
Prohan350 wrote:

Meta-RNA is good and that's what I typically used but there's also Phyloshop:

http://omics.informatics.indiana.edu/mg/phyloshop/

ADD COMMENTlink written 8.7 years ago by Prohan350

Phyloshop appears to use the HMMs from MetaRNA(H3) (http://weizhong-lab.ucsd.edu/metarna/) with HMMer, so really doesn't provide a distinct de novo rRNA gene finding system.

ADD REPLYlink modified 6.9 years ago by Michael Dondrup46k • written 8.4 years ago by Casey Bergman18k
2
gravatar for Casey Bergman
8.4 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

You can also try RNAmmer for de novo rRNA gene prediction. See paper here: http://nar.oxfordjournals.org/content/35/9/3100.abstract

ADD COMMENTlink written 8.4 years ago by Casey Bergman18k

It looks like RNAmmer is not suited to the shorter 454 reads...

"most of rRNA genes in metagenomic sequencing reads are fragmentary, and will be overlooked by RNAmmer that focus on full length rRNAs. "

From the introduction of http://bioinformatics.oxfordjournals.org/content/25/10/1338.full suggested by TreyLathe

ADD REPLYlink written 8.3 years ago by Aarons80
1
gravatar for Casey Bergman
8.3 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

There is a new covariance model based method for SSU detection from the Eddy lab, called SSU-ALIGN.

SSU-ALIGN is a tool for aligning, masking and visualizing archael 16S, bacterial 16S and eukaryotic 18S small subunit ribosomal RNA (SSU rRNA) sequences. The package includes a user's guide with a tutorial. SSU-ALIGN is described in part 2 of Eric Nawrocki's Ph.D. thesis "Structural RNA Homology Search and Alignment using Covariance Models."

ADD COMMENTlink written 8.3 years ago by Casey Bergman18k
1
gravatar for Marina Manrique
8.3 years ago by
Marina Manrique1.3k
Granada
Marina Manrique1.3k wrote:

For 16S rRNA genes I like the RDP (Ribosomal Database Project), you can download the unaligned sequences in FASTA format here

ADD COMMENTlink written 8.3 years ago by Marina Manrique1.3k
1
gravatar for Johan Bengtsson
8.0 years ago by
Johan Bengtsson10 wrote:

For accurate identification and classification of different kinds of SSU sequences (both 12S, 16S and 18S) in metagenomic data, I would recommend using our newly released package called Metaxa ( http://microbiology.se/software/metaxa ), which works like a charm on metagenomic 454 data. See this page for the accompanying paper: http://www.springerlink.com/content/n56h854713187159/

Good luck!

ADD COMMENTlink written 8.0 years ago by Johan Bengtsson10
0
gravatar for Prateek
8.4 years ago by
Prateek1.0k
Boston, MA
Prateek1.0k wrote:

Check out this paper

<http://sigen.org/index.php/sigen/article/view/sigs.651139/192>

describing J. Craig Venter Institute's metagenomic data processing pipeline. They processed some of the largest metagenomics datasets including Global Oceans Sampling (GOS)

ADD COMMENTlink written 8.4 years ago by Prateek1.0k
0
gravatar for k09im01
4.2 years ago by
k09im010
United States
k09im010 wrote:

You might also consider using the EMIRGE program to reconstruct all 16S rRNA genes.  That's how I've been fishing that info out of my metagenome data (from shotgun Illumina reads). I've believe it outputs fasta sequences.

Here's a link to the paper: http://genomebiology.com/2011/12/5/r44 - "EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data" 

And the link to git hub repository: https://github.com/csmiller/EMIRGE/blob/master/emirge.py

ADD COMMENTlink written 4.2 years ago by k09im010
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