DREME (Discriminative Regular Expression Motif Elicitation) finds relatively short motifs (up to 8 bases) fast, and can perform discriminative motif discovery if given a negative set, consisting of sequences unlikely to contain a motif of interest that is however likely to be found in the main ("positive") sequence set. If you do not provide a negative set the program shuffles the positive set to provide a background (in the role of the negative set).
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- To use DREME, import your data in fasta format.
- Resources: http://meme.sdsc.edu/meme/doc/dreme.html
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> iplant_training -> advanced_chip-seq
Use fastaFromBed_out.fa from the directory path Community Data -> iplantcollaborative -> iplant_training -> advanced_chip-seq -> 03_best_summits_slop100_fastaFromBed as test input.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Default parameters only, no further configuration needed.
Expect several files as output. For the test case, the output files are located in the directory Community Data -> iplantcollaborative -> iplant_training -> advanced_chip-seq -> dreme -> dreme_out .