Finding motif in DNA sequence region

[boyangwhite]

Hi, All,
I'm a new PhD student in this field, and new here. I found many amazing stuffs in this Forum.

Now, I'm involving into a project which require me to find the TF binding in a set of DNA region.
What I know are the DNA regions' location and sequence, the length of them are around several kb to 100 kb.
Is there a tool to find the enrichment TF binding motifs in these region? As I know, the MEME and DME are designed for chip-seq data whose length is about only several hundred bp, so can these tools be used for my purpose?

Thanks

[mikep]

Meme will look for enriched motifs in your sequence, no guarantees said motifs mean anything, or represent any particular TF. transfac will look for known TF sites in your data and report them, problem being most TFs have small recognition sites so you tend to get a mountain of false positives.

Problem with both is performance degrades with increasing input length, the chances of either doing anything meaningful on a sequence of 100kb are slim.

My advice would be to do an overlap with empirical data, such as ENCODE. You still have the problem of... "biochemically active vs functional", but that's a step up from prediction false positive.