multiple Sequence Alignment tools for cis-element
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3 months ago

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. enter image description here

Best wishes

Guandong Shang

MSA cis-element • 192 views
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Entering edit mode
3 months ago

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, ...

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