Hello everyone, I have the complete genome sequence of a bacterium in an assembly form. How can I easily and practically determine which strain it is? Also, how can I find the 16S rRNA of this bacterium? Thank you.
Jakub Grzesiak
Annotate the genome using PATRIC website, download the Excel sheet, search for the SSU sequence and BLAST it.
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Abhijeet Singh
If you are trying to identify a bacterial candidate at strain level, probably that would not be possible considering your level of experience and procedure/method required for the job and the way question is written here. It is just that you need to have some guidance. When you say "strain" is it really strain you you want to identify the bacteria at genus or species level? If you have the sequence from an isolate, probably you already know the identity of the bug. With just 16S sequence, identification at strain level is probably not possible As suggested above, you can try it but in my experience you will probably not get the answer you are looking for. Suggestion one will take some efforts and suggestion two is not that accurate. In addition to suggestions above, you can try to taxonomically classify the genome at KBase using GTDBtk.
Few points which need to be mentioned as prerequisite:
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