EMSA is often compared to techniques like Chromatin Immunoprecipitation (ChIP) and DNase I Footprinting. While ChIP is used to study protein-DNA interactions in living cells, providing in vivo context, EMSA is an in vitro assay that offers higher sensitivity and specificity. DNase I Footprinting, on the other hand, precisely identifies the binding site on the DNA, but EMSA is simpler and faster to perform.