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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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  • $\begingroup$ You could look into ChIP-Seq $\endgroup$
    – canadianer
    Commented Apr 28, 2014 at 16:53
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    $\begingroup$ Identify it as what? Guess the species of origin? Guess the individual it came from? Guess its function? $\endgroup$
    – terdon
    Commented Apr 28, 2014 at 18:53
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    $\begingroup$ Since he is talking about footprinting, I assume he wants to identify what motif a particular protein binds. $\endgroup$
    – canadianer
    Commented Apr 28, 2014 at 19:34
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    $\begingroup$ @canadianer ah! DNAse footprinting, OK. $\endgroup$
    – terdon
    Commented Apr 28, 2014 at 21:38

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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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