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Old 08-13-2012, 12:40 AM   #1
Mithril
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Default 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!
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Old 08-15-2012, 04:38 PM   #2
themerlin
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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.
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Old 08-19-2012, 09:26 PM   #3
Mithril
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Thank you for the tool, ill check it out!
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Old 09-23-2012, 02:05 AM   #4
faozhi
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or EMIRGE? https://github.com/csmiller/EMIRGE
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