Motif seq in input seq and genes

I have identified a chip seq motif. How I can identify occurrences with statistical significance in the number seq that I used to identify such motif. I also want to identify occurrences of this motif in number of genes (names). What tool can be best used for this purpose?

Thanks

chip-seq

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updated 8.8 years ago by ivivek_ngs

• written 8.8 years ago by kanwarjag

2 answers

MEME can be used to (re)identify the motif and evaluate its statistical significance. MAST can be then used to search for the motif in other regions of the genome. http://meme-suite.org/

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written 8.8 years ago by Asaf

For sequences as Asaf highlighted MEME is good. For genes I would highlight 3 other. HOMER, PSCAN and iRegulon.

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written 8.8 years ago by ivivek_ngs

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