How to get a publication quality image from AME analysis?

[Hyun Jung Park]

Hello, 

I just ran AME analysis on the webserver using my motif of interest, and successfully got the result (thank you MEME team). 

However, the problem is that I can't use the logo in the AME HTML output, because it is too low resolution. 

I right-clicked and saved it in png, but it is still low resolution. 

And I can't figure out another way to export high resolution logogram (I also looked at other sections in the result file). 

Can you please show me how to export a high resolution logogram out of this HTML result? 

Thanks, 

HJ

[CharlesEGrant]

Hi HJ,

There isn't anyway to create a public quality logogram directly from the AME output.

 If you are using one of the provided motif databases try following the link from the motif to the source database. Some of the motif databases, like JASPAR, will provide logograms in SVG or other publication ready format. 

If the input motif file was generated in a MEME run, you can generate a publication quality logogram from the MEME HTML output file:

1. Open the MEME HTML file in your web browser
   
2. In the "Discovered Motifs" section, click on the "Submit/Download" arrow for the motif of interest.
   
3. Click on the "Download Logo" tab.
   
4. Set the format to "EPS"
   
5. Click on the "Download" button.
   

If you don't have the MEME HTML file, you can generate a logogram from a plain text MEME file using the ceqlogo utility. This utility is not available on the public web site. You'll nee to install a local copy of the MEME Suite. The source for the MEME Suite can be downloaded here. The installation guide can be found here.