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Hi! I'm new in this and I'm learning about how to use, databases, Python, Jupyter Notebook... So I want to know how to form an epitope taken from a bacterium, put it into some database o something and search if some microorganism in our gut, has this epitope ins his proteins. I will consider any type of advice or counsel I will thank you. Thank you for your attention, M.O.D
The project you describe could easily be a PhD project. I would recommend starting with some smaller tasks and understanding the underlying biology before undertaking such an ambitious task.
But you know how to do it??? The only thing that I want to know is that if there is a database to search for what gut bacteria has a specific epitope. i know its difficult, but I have to do it...
What kind of epitope? If you want to know if a bacteria in our guts has a particular protein for example, that's pretty easy to figure out.
You've phrased this idea in a way that makes it sound straightforward but as Jared pointed out, depending on your meaning, it most likely won't be.
Basically what I'm doing is finding a bacteria in the human intestine that contain in their proteins an epitope (which I have previously taken from another protein of a bacterium) But, how do you do to know if a bacteria in our guts has a particular protein??????
Probably poke around the check the Ensembl databases for the bacteria in question and try to determine if it has a homologous gene (this is often not all that straightforward). BLAST will probably come in handy. Determining whether it has the epitope or not is another question entirely, and one that I don't have the expertise to answer.
Find a metagenomic gut sample (microbiome) project in NCBI (if you don't have your own data) that you trust. Given that we still know very little about a 'typical' microbiome, deciding what data to use has no right answer at the moment so you'll need to make some assumptions probably.
Then simply get all the protein sequences from all the genomes, and look for your epitope. Simplest thing that springs to mind would be to make a
blastdatabase of that set of genomes, andblastpagainst it with your epitope.