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6.3 years ago
sharmatina189059
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110
Dear all I have a 3000 genes of a reference genome of bacteria and I need to find out their protein-protein interactions.I have performed blast of these 3000 genes with its closest species which has been annotated in STRING database and extract protein sequences shows > 98% seqeunce similarity. Now based on this alignment, I need to extract their interacting partners, score, type of interaction, co-expressed genes, organism with co-expressed genes and assay performed. I am new to this field. Can anybody help me out doing this?
Not sure what your problem is here. If you have identified proteins present in STRING, just extract from STRING the interactions containing these proteins. You can download STRING data here. However, STRING doesn't contain information on the type of assay. For this you'll have to go to other resources. For example for the type of assay used to determine physical protein interactions, you'll have to go to the source databases used by STRING (e.g. IntAct, BioGRID, ...)