How to map protein interaction from different species?

Question

[joycewang83]

Hi all,

I would like to plot potential interactions of proteins from two bacterial species (we study horizontal gene transfer)

String-db only maps proteins from one single species under protein mode, and COG mode gives a big spiderweb which is hard to interpret.

Does anyone have any suggestions? I have about 300 proteins so a software that accepts batch submission would be great.

Thanks, Joyce

Answer 1

[Whoknows]

Hi

You can use String-db.org, string-db is very powerful and good in this ,it can create a PPI based on your proteins and you can filter the type of detection in PPI. String also create and visualize network based on the output genes in Graphical format or Text format which could be applicable in Cytoscape. You can search in String-db in batch mode.

Please take look at [Ingenuity IPA], IPA is not free but you can use trial for a week, IPA has a very complete data on human protein protein interaction network, IPA accept batch protein list

enjoy!!

Answer 2

[5utr]

If you already have the list of potential interactions you can import them in Cytoscape and use the different layouts to reduce the "spiderweb" effect.

[joycewang83]

Thank you Gian for your suggestion. While the spiderweb effect couldn't be eliminated (simply too many COGs), at least now there's a new way to present the data! Thanks!

Joyce