How to perform PPI network analysis in STRING for newly sequenced bacterial genome ?
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5 weeks ago
Kumar ▴ 50

I need to perform Protein-Protein Interaction (PPI) networks analysis for newly sequenced Xanthomonas genus bacteria on STRING tool. But, our Xanthomonas genus bacteria is not listed in the STRING database. However, other Xanthomonas genus bacteria are listed in the STRING database. Therefore, Please help me how to proceed my analysis. Should I choose the closely related Xanthomonas genus bacteria available in the STRING database or is there any other way to do the same?
Please help me in this cause.

Thank you in advance.

Proteomics cytoscape network STRING • 120 views
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5 weeks ago
Scooter ▴ 100

Greetings, Well, you know your species better than us. Unless you suspect that there has been significant network rewiring between the two species, starting with a closely related one makes sense. Ideally, that will be a good starting point and any interactions of interest can be more closely probed by looking at the sequence differences between the proteins to determine if there are significant changes that might result in changes to binding.

-- scooter

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