Tool To Generate Motif Diagrams

Question

[Nickengland]

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! :)

[Niallhaslam]

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.

Answer 1

[Niallhaslam]

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/

Answer 2

[Neilfws]

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.