RNA motifs in TomTom?

[Tina O'Grady]

Until recently I was able to use Tomtom on the web server to compare my motifs to the Ray2013 or CISBP-RNA databases of known RBP motifs. Now I only see options for databases of known DNA motifs. What happened? Is it still possible to use the RNA motif databases? I tried looking at older MEME suite versions too, and couldn't find them.

Thank you for your help!

-Tina

[Rocky Parida]

You can download all the motif databases for MEME from http://meme-suite.org/doc/download.html?man_type=web.
Then you can download meme command line version and try using tomtom from command line via this command

Usage:

tomtom [options] <query motifs> <target motif database>+

<query motifs> I use meme to generate motifs so I use this meme.txt file here, but whatever motif matrix format you can use here following http://meme-suite.org/doc/meme-format.html. There programs can help you in converting your files into MEME format http://meme-suite.org/doc/overview.html#motif_conversion_utilities.

<target motif database> Assuming you are using a specific organism then just give the path to that organism's name.meme file in your CISBP-RNA folder (part of motif database download).

Hope this helps.
Rocky

[CharlesEGrant]

Hi Tina, the RNA motifs were lost in a recent update of the motif databases. We should have them back online soon.

[Tina O'Grady]

Thank you, Rocky and Charles!