Would it be possible to download the (All Drosophila) database in MEME format for running TOMTOM locally?

[Margaret H]

Would it be possible to download the (All Drosophila) database in MEME format for running TOMTOM locally?

I know that direct downloads are available from various sources that comprise the MEME All Drosophila database,such as Fly Factor Survey, etc. in PFM/PWM form but if the motifs already exist in correct MEME PSPM format on the MEME servers, is there a way that I can download the data in this format?

Thanks,
Margaret

[James Johnson]

The "All Drosophila" option is a group of databases. Specifically it uses the databases:
fly_factor_survey.meme
flyreg.v2.meme
idmmpmm2009.meme
dmmpmm2009.meme

Which are all included in the motif databases download available at:
http://ebi.edu.au/ftp/software/MEME/index.html

If you want to determine what databases are in each option you can open the motif_db.csv file in any text editor and look at the space separated file names before the first comma on each line.

You can run Tomtom with all the fly databases with the command:
tomtom query.meme fly_factor_survey.meme flyreg.v2.meme idmmpmm2009.meme dmmpmm2009.meme

The full command-line documentation for Tomtom is available here:
http://meme.nbcr.net/meme/doc/tomtom.html