motif genome wide

[Liy]

Hi all,

Can someone tell me how to get all the coordinate of a sequence motif coordinate genome wide? Prefered output is bed format.

Thanks!
L

[TiborNagy]

It is depends on what kind of motif format do you have
Homer has a program (findKnownMotifs.pl), which use matrix, but fuzznuc (part of the Emboss package) use consensus sequence as query.

[GenoMax]

@Liy: Just to be clear about what you are asking.

You know the motif you want to get corresponding coordinates for (genome wide) with output in BED format.

[crazyhottommy]

Hi all,

Can someone tell me how to get all the coordinate of a sequence motif coordinate genome wide? Prefered output is bed format.

Thanks!
L

You may download from here http://compbio.mit.edu/encode-motifs/