extract 16sRNA genes from assembled contigs

Question

[serene.s]

Hi Everyone!

Does anybody know how can I extract only the 16sRNA genes from metagenomic contigs which have been assembled already using MegaHit? Basically, these are .fasta format contigs so what are the tools that can do this job of extracting the 16sRNA sequences from the assembled contigs.

Thanks

Answer 1

[Mensur Dlakic]

I think this is the best choice as it will detect discontinuous sequences (some 16S rRNAs have introns or homing endonucleases). However, it is slow.

http://eddylab.org/software/ssu-align/

If you are more interested in speed:

https://github.com/tseemann/barrnap

[serene.s]

thanks for your response Mensur Dlakic :-)