Dear experts,
I want to extract a bacterial complete 16S rRNA gene sequence from WGS (Whole-genome sequence). I have a bacterial WGS (FASTA file=assembled scaffold's FASTA) with 6857405 bp that was divided into 22 Scaffolds.
Can you suggest to me that how can I easily know/extract the complete 16S rRNA gene sequence from WGS ? Is there any software or online tools?
Thank you so much.
Balig Panossian
BARRNAP (command-line ) https://github.com/tseemann/barrnap Web-based tools (NB: each with their own caveats)
Md. Amdadul Huq since your genome is already assembled, I recommend you use one of the following tools:
- SortMeRna (currently under maintenance) https://bioinfo.lifl.fr/RNA/sortmerna/
- RNAmmer 1.2 (only accepts up to 1 million bp, try feeding it from the bottom of your fasta file, the 16s is usually assembled with poor contiguity, and will be at the bottom of the assembly file ) http://www.cbs.dtu.dk/services/RNAmmer/
- Rfam - https://rfam.xfam.org/ ( quite comprehensive, explore and know what you're doing )
- Bonus tip, if all else fails, you can annotate your assembly by uploading it to RAST tk https://rast.nmpdr.org/ and you should be able to fish out the 16s via the web interface
hope this helps !
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