Is there a next generation sequencing technique that I can apply? It would be nice if I can identify all the parasite proteins that bind at once and the DNA location of the host.
Hi....
If you have antibody available for parasite protein then you can use chip-seq to identify the dna sequence in host where parasite protein binds.
I don't know which parasite proteins are interacting with DNA, that's my goal
Does the parasite have any closely related species that is characterised? You could use the genomic information to model a ligand-protein interaction de-novo. That may reduce the targets pairs you have to look at. Also .. you could run a Chip-Seq analysis of the infected tissue after you have these target pairs, and then reduce interactome density using the now present host data.. Still a daunting task though..
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