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Since DNA footprinting is an old method I thought there may be some more recent and effective methods to identify a DNA sequence, do you know any of them?

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You could look into ChIP-Seq – canadianer Apr 28 '14 at 16:53
Identify it as what? Guess the species of origin? Guess the individual it came from? Guess its function? – terdon Apr 28 '14 at 18:53
Since he is talking about footprinting, I assume he wants to identify what motif a particular protein binds. – canadianer Apr 28 '14 at 19:34
@canadianer ah! DNAse footprinting, OK. – terdon Apr 28 '14 at 21:38

DNAse-seq is the most obvious choice. It uses the same idea as DNAse footprinting but measures output using high-throughput sequencing, so it can be done on a whole genome in one shot.

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DNA sequencing, RFLP, IHC, In Situ Hybridization, Southern Blotting.

I think the technique you are looking for (what you are talking about), is an Electro Mobility Shift Assay or EMSA

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