Hello reader;
Hope so you are doing well. I have 16S RNA sequences of some bacterial species and I want to Identify glycoside hydrolases gene in those species. I want to know that is there any technique used in bioinformatics to identify those gene family using the 16S RNA sequence.
Looking for your knowledge .
Thank You.
Hi Umar,
You can retrieve the sequences for glycoside hydrolase gene from NCBI once you have identified your concerned species on the basis of 16S rRNA. The only catch here can be whether the sequence for the specific genes is available in NCBI or not.
Best Wishes
Pankaj
Dear Omar
If you could identify the species of your bacteria by have the 16s sequence of your desired species, you may look up at the reference sequence of that species on NCBI. There are a large number of bacterial ref seqs with annotation deposited there. Then you may easily browse the genome and find the glycoside hydrolases gene.
Best of luck
Hi Umar,
You may need first to classify the 16S Gene using our taxonomic classifier tool AmpliconNet
https://github.com/ali-kishk/AmpliconNet
You will need to download the repo and use V46 model in the prediction example.
Then you may continue with @Ali Javadmanash suggestion.
You'll be able to find it by doing a BLAST search for the hydrolase gene in your bacteria of interest. But as others have said, that assumes that your bacteria has been sequenced. If not, you'll have to either go hunting for the glycoside hydrolases gene using PCR primers designed from related species and/or sequence the entire genome of your bacteria.
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