Usage (Python 2.7):

dreme [options] -p <primary sequence file> [-n <control sequence file>]

Usage (Python 3.x):

dreme-py3 [options] -p <primary sequence file> [-n <control sequence file>]

Description

Two different versions of Dreme are provided: dreme for Python 2.7 and dreme-py3 for Python 3.x. The random number generator has changed between Python 2.7 and Python 3.x, so results between the two verisons may differ if you don't explicitly provide a control sequence file.

Input

Sequence file (primary)

A collection of sequences in FASTA format. The sequences should all be approximately the same length.

Output

DREME writes an XML file to the output folder and converts it into a minimal MEME-formatted motif file and a human readable html file.

Additionally DREME can output motif logos if the -png and/or -eps options are specified.

Options

OptionParameterDescriptionDefault Behaviour
Input/Output
-pprimary sequence file The name of a file containing the primary sequences in FASTA format. Required argument.
-ncontrol sequence file The name of a file containing the control sequences in FASTA format. DREME will create a set of control sequences by shuffling the primary sequences while preserving dimer frequencies.
-png  Output motif logo images in portable network graphics (png) format. This format is useful for display on websites. Images are not output in png format.
-eps  Output motif logo images in Encapsulated Postscript (eps) format. This format is useful for inclusion in publications as it is a vector graphics format and can be easily scaled. Images are not output in eps format.
Alphabet
-dna  Use the standard DNA alphabet. This is the default alphabet anyway so the option only exists for symmetry. The standard DNA alphabet is used.
-rna  Use the standard RNA alphabet. The standard DNA alphabet is used.
-protein  Use the standard protein alphabet. This does not work very well because the protein alphabet only has 3 ambiguous symbols which does not cover the range of possibilities very well at all. The standard DNA alphabet is used.
General
-norc  Search only the given primary sequences for motifs. Search the given primary sequences and their reverse complements for motifs when the alphabet is complementable.
-gngen Set the number of REs to generalize. Increasing ngen will make the search more through at some cost in speed. DREME will generalise 100 REs.
-sseed Set the seed for the random number generator used to shuffle the sequences. When the -n option is given the control sequences will be used instead of shuffling. The random number generator is initilised with a value of 1.
Stopping Conditions
-ee Stop searching for motifs when the next motif's E-value is > e. Stop discovering motifs if the E-value threshold of 0.05 is exceeded.
-mm Stop searching for motifs when m motifs have been found. There is no limit on the number of discovered motifs.
-tt Stop searching for motifs when t seconds have elapsed. There is no limit on the time taken to discover motifs.
Set Core Motif Width
-minkmink Set the minimum width of the motif core. A minimum core width of 3 is used.
-maxkmaxk Set the maximum width of the motif core. A maximum core width of 7 is used.
-kk Set the width of the motif core. This sets minimum width and maximum width to the same number. The defaults for minimum and maximum width are used.
Miscellaneous
-desc description Include the text description in the HTML output. No description in the HTML output.
-dfile desc file Include the first 500 characters of text from the file desc file in the HTML output. No description in the HTML output.
-h  Display a usage message and exit. Run as normal
-version Display the version and exit. Run as normal.
Experimental (use at own risk)
-l  Print list of enrichment of all REs tested.  

Citing

If you use DREME in your research please cite the following paper:
Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. [full text]