Finding Rrna Genes In Metagenomic Data
8
11
Entering edit mode
10.8 years ago
toshnam ▴ 650

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.

metagenomics rrna database rna • 9.4k views
ADD COMMENT
3
Entering edit mode
ADD REPLY
0
Entering edit mode

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

ADD REPLY
9
Entering edit mode
10.8 years ago
Treylathe ▴ 950

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 COMMENT
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
10.8 years ago
Prohan ▴ 350

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

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

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
2
Entering edit mode
10.5 years ago

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

ADD COMMENT
0
Entering edit mode

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 REPLY
1
Entering edit mode
10.5 years ago
Prateek ★ 1.0k

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 COMMENT
1
Entering edit mode
10.4 years ago

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 COMMENT
1
Entering edit mode
10.4 years ago
Marina Manrique ★ 1.3k

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

ADD COMMENT
1
Entering edit mode
10.1 years ago

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 COMMENT
0
Entering edit mode
6.3 years ago
k09im01 • 0

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 COMMENT

Login before adding your answer.

Traffic: 2439 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6