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.
Here are are a few:
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
•
written
by
Treylathe •
The method Trey refers to is Meta-RNA: http://weizhong-lab.ucsd.edu/meta_rna/
•
written
by
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.
•
written
by
Casey Bergman
•
written
by
Casey Bergman
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
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)
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.
•
written
by
Casey Bergman
For 16S rRNA genes I like the RDP (Ribosomal Database Project), you can download the unaligned sequences in FASTA format here
•
written
by
Marina Manrique
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!
•
written
by
Johan Bengtsson •
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
There is currently a tools called ribodetector
Log in to answer this question.
See previous question "Where do I find the 16S rDNA reference sequences (metagenomics)"
Oh didn't see this. Some good answers there including green genes :)