I have the sequence of a Pseudomonas strain. I can predict transcription factors during annotation using EMBOSS. What I'm missing now is the prediction of transcription factor binding sites and the connection between both.
I think one way would be: Blast the TF against a curated database of a related strain and choose the best fitting TF with it interactions. Blast all the genes it's interacting with against my genome. This way I could map the interactions of the related strain to my strain.
But this would be a lot of work and I don´t know if there is a database to blast against. Is there maybe a tool, that can do that?