How to find motif in specific region

Question

[zhang616123]

Hi,

Assume I have got a list of motif some protein could binding (for example, by chip-seq). Now I have some interestion genomic region (one or more, but very limited), is it possible to know to know whether these intervals exist and which known motifs exist?

Answer 1

[Alex Reynolds]

You could use FIMO to discover binding sites from MEME motif probability tables: https://meme-suite.org/meme/doc/fimo.html