I have a research project for this semester and I wanna do about a bacteria. I want to look for the region of virulence factor, but then I'm not sure what is the next step (what I wanna know about the virulence factor since it has many example of virulence factors). It is undergraduate research. Ideas needed, thanks!
You could align the sequences for the virulence factor(s) of interest and construct a maximum likelihood phylogenetic tree. If you have metadata (phenotypic data etc) for the organisms from which the sequences were obtained, you could overlay these on the tree and see if you can observe some patterns such as clade associated with certain phenotypes etc. You could then use this information to identify the specific base changes in the sequence alignment that are associated with the observed pattern in the tree.
There are many db containing proteins involved in virulence: How To Find Proteins Related To Patogenicity Of A Bacteria ? or also PHI-base.
However, I will focus on which factor you want consider. This might help you to make a more focus and precise project. You can start reading some papers and reviews on this topic.
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I was thinking to do abt polysaccharide capsule of the bacteria, which is one of the virulence factor as well. But what's next? Is it possible to do phylogenetics analysis of the polysachharide capsule of the bacteria ? I'm lost. Thanks
Well, best thing you can do is look for papers on this matter. I think this will be the best way of helping yourself.