Hello Everyone,
I have whole genome sequence of bacteria (which I want to prove as a novel spp. and 99% novel). I want to extract the 16s rRNA gene sequence from it digitally. What is the easiest method to do that?
P.S:In the past, I did you Truebac app from Ezbiocloud and it was pretty easy but I guess, they do not allow more than two genomes to evaluate freely? (Perhaps, i need to pay after analzing two new genomes)? In short, I am not able to use Trueback to analyze another new genome.
Best regards,
Timsy
Maybe my answer is very late, but for other student, i used a very easy method at Ezbiocloud I used the tool ContEst16S, it can help to extract 16s fragments.
There are several ways to extract 16s sequences from the genome
- annotate the genome and in annotated genbank format see if there are any full length 16s sequences. Extract them from genbank file (manual copy paste) and save as fasta squence
- blast can be used to get the aligned part of 16S sequence from genome query. Reference must be good and a bit knowledge required to interpret blast result
- MSA can also be done to get the alignment between 16S from query and a set of reference dataset
- and ofcourse, as suggested above
In my case, upload in RAST annotation server and download results as excell file. Then, you can get 16S rRNA gene sequences.
Hi. The following procedure might help: annotate genome on PATRIC, click on 'view annotated genome', and you can see rRNA genes in the genomic features table.
Ola Alessa Wow, thanks!!! This tool is amazing. Needed this badly right now! So glad I found your answer. Thank you for sharing.
If the query sequence was from a MAG, it is no surprise that no 16S sequence could be detected. And it simply mean that there was no 16S assembled in the MAG during processing.
It is not the tool thing but the MAG related thing. Many MAGs do not contain 16S, while some does.
In case you don't find 16S, try using some other marker gene.
- Badges
- Science topic
- Similar topics
- Phytochemistry
- Extracts