Finding Rrna Genes In Metagenomic Data

Question

[toshnam]

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.

[Pierre Lindenbaum]

See previous question "Where do I find the 16S rDNA reference sequences (metagenomics)"

[Treylathe]

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

Answer 1

[Treylathe]

Here are are a few:

• Green genes has 16s rRNA
• Silva is an rRNA database you can blast

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

[Casey Bergman]

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

Answer 2

[Prohan]

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

[Casey Bergman]

Phyloshop appears to use the HMMs from Meta_RNA(H3) with HMMer, so really doesn't provide a distinct de novo rRNA gene finding system.

Answer 3

[Casey Bergman]

You can also try RNAmmer for de novo rRNA gene prediction. See paper here

[Aarons]

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

Answer 4

[Prateek]

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

Answer 5

[Casey Bergman]

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.

Answer 6

[Marina Manrique]

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

Answer 7

[Johan Bengtsson]

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, which works like a charm on metagenomic 454 data. See this page for the accompanying paper

Good luck!

Answer 8

[k09im01]

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

Answer 9

[georgekitundu2]

There is currently a tools called ribodetector