multiple Sequence Alignment tools for cis-element

Question

[shangguandong1996]

Hi, everyone.

I am wondering whether there is a tool designed for do MSA for nocoding DNA, like cis-element. I want to find whether there is a conserved module shared by several cis-element identified by ATAC-seq or H3K27me3, which located nearby same gene.

For example, there are so many peaks located near this gene.

Best wishes

Guandong Shang

Answer 1

[lieven.sterck]

Yes there are.

If you google for "phylogenetic footprinting" you should find most of them I assume. (or perhaps even motif alignment or such)

Some from the top of my head: MEME, RSAT suite, Di-Aligner, ...