Question: Tool To Generate Motif Diagrams
1
gravatar for Nickengland
8.5 years ago by
Nickengland130
Nickengland130 wrote:

I have seen diagrams for representing binding sites of proteins to DNA which shows 2 bases either side of the target site, with the vertical axis split into 4 different areas, A/C/T/G. The size of these letters corresponds to the ratio of that base in that position.

A couple of different papers had very similar diagrams which leads to be believe there is probably some tool to generate these? Does anyone know what it is? I couldn't find it referenced in the papers.

Thanks! :)

motif dna • 1.9k views
ADD COMMENTlink modified 8.4 years ago by Neilfws49k • written 8.5 years ago by Nickengland130
1

Could you post an example or a link to one of the papers you mention? Also motif is spelt wrong in the title and the tags.

ADD REPLYlink written 8.5 years ago by Niallhaslam2.3k
5
gravatar for Niallhaslam
8.5 years ago by
Niallhaslam2.3k
Dublin
Niallhaslam2.3k wrote:

It could be using the bioconductor package: http://bioconductor.org/packages/2.2/bioc/html/seqLogo.html

Or the weblogo software: http://weblogo.berkeley.edu/

ADD COMMENTlink written 8.5 years ago by Niallhaslam2.3k
4
gravatar for Neilfws
8.5 years ago by
Neilfws49k
Sydney, Australia
Neilfws49k wrote:

As Niall said, WebLogo is commonly used for this. Also check out the MEME suite for useful motif-related tools; TOMTOM is one which generates sequence logos.

ADD COMMENTlink written 8.5 years ago by Neilfws49k
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