Tool to identify 16s rRNA fragments in raw data

Mithril · 08-13-2012, 01:40 AM

Hello,
I have metagenome data samples in FASTA format downloaded from EBI and CAMERA. I wanted to extract 16s rRNA fragments from this FASTA file. Can anybody tell me how exactly to go about doing this? I am new to this and have very little guidance.

I did look at Metaxa http://microbiology.se/software/metaxa/
However, the software requires a profile of bacterial and archeal organisms. How do I obtain this?

Thank you for your time!

themerlin · 08-15-2012, 05:38 PM

You could try SSU-align

http://selab.janelia.org/software.html

Works well on whole genome data to pull out 16S, but I don't know how slow it would be on large metagenome datasets.

Mithril · 08-19-2012, 10:26 PM

Thank you for the tool, ill check it out!

faozhi · 09-23-2012, 03:05 AM

or EMIRGE? https://github.com/csmiller/EMIRGE

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08-13-2012, 01:40 AM	#1
Mithril Member Location: Vienna Join Date: Apr 2012 Posts: 12	Tool to identify 16s rRNA fragments in raw data Hello, I have metagenome data samples in FASTA format downloaded from EBI and CAMERA. I wanted to extract 16s rRNA fragments from this FASTA file. Can anybody tell me how exactly to go about doing this? I am new to this and have very little guidance. I did look at Metaxa http://microbiology.se/software/metaxa/ However, the software requires a profile of bacterial and archeal organisms. How do I obtain this? Thank you for your time!

08-15-2012, 05:38 PM	#2
themerlin Member Location: Flagstaff, AZ Join Date: Feb 2010 Posts: 51	You could try SSU-align http://selab.janelia.org/software.html Works well on whole genome data to pull out 16S, but I don't know how slow it would be on large metagenome datasets.

08-19-2012, 10:26 PM	#3
Mithril Member Location: Vienna Join Date: Apr 2012 Posts: 12	Thank you for the tool, ill check it out!

09-23-2012, 03:05 AM	#4
faozhi Junior Member Location: Australia Join Date: Dec 2011 Posts: 5	or EMIRGE? https://github.com/csmiller/EMIRGE