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.
There are really two approaches to do what you want. First, you can create a custom proteome in string using your new species:
Proteome Annotation / Adding new species to STRING
You can now add your proteome to STRING. On the input page under “Annotate your proteome”, you can now add completely new (or existing) species to STRING. The only data that is required is a FASTA file with the proteins in your organism (one protein per gene), and the clade name of the added proteome. STRING will then compute both functional and physical interaction networks, as well as functional annotation (among others GO and KEGG) of all the proteins in your proteome. Your proteome can be then browsed through the web interface in the same way as any other species in STRING. The data can be also accessed via API or downloaded on the STRING’s download page. You can also share your proteome with anyone using the provided species identifier (starts with the letters “STRG”).
The new species can be accessed by the stringApp using the provided species identifier.
The other approach would be to use the related genus, assuming that the gene names (not the gene identifiers) map between the two related species.
Hi. How did you do it? I’m facing kind of similar situation. Thank you so much.