Motif Logo

[jpu...@broadinstitute.org]

Hi,

The MEME suite has very nicely formatted motif logos, but unelss I do something like TOMTOM I haven't been able to get a high quality for the motif itself. If I'm doing CENTRIMO and I want to show the motif that is being enriched, is there a good way to download the motif logo itself? So If I'm showing a TF motif is centrally enriched, how do I get that TF's motif logo in high quality.

Thanks!

[CharlesEGrant]

Centrimo doesn't contain any direct facility for generating publication quality logograms. If these are motifs that you generated yourself using MEME, then the MEME HTML output file contains Javascript code for generating logos in Encapsulated PostScript (EPS) format. See the posting How can I get publication quality copies of logograms? for more information. 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 that isn't adequate, you could  install a local copy of the MEME Suite, a local copy of the motif library, and use the ceqlogo utility to generate logograms in EPS format.

Charles

[James Johnson]

To add to Charles' answer. All the motifs database that are used by CentriMo on the website are also available for download here:
http://meme-suite.org/doc/download.html

You should be able to match up the file names and motif id's from the CentriMo output and make use of either meme2images ( http://meme-suite.org/doc/meme2images.html ) or Ceqlogo ( http://meme-suite.org/doc/ceqlogo.html ). Note that meme2images is probably easier to use than CeqLogo but it will generate logos for every motif in the file at once.