dreme [options] -p <primary sequence file> [-n <control sequence file>]
dreme-py3 [options] -p <primary sequence file> [-n <control sequence file>]
dremefor Python 2.7 and
dreme-py3for 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.
A collection of sequences in FASTA format. The sequences should all be approximately the same length.
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.
|-p||primary sequence file||The name of a file containing the primary sequences in FASTA format.||Required argument.|
|-n||control 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.|
|-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.|
|-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.|
|-g||ngen||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.|
|-s||seed||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.|
|-e||e||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.|
|-m||m||Stop searching for motifs when m motifs have been found.||There is no limit on the number of discovered motifs.|
|-t||t||Stop searching for motifs when t seconds have elapsed.||There is no limit on the time taken to discover motifs.|
|Set Core Motif Width|
|-mink||mink||Set the minimum width of the motif core.||A minimum core width of 3 is used.|
|-maxk||maxk||Set the maximum width of the motif core.||A maximum core width of 7 is used.|
|-k||k||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.|
|-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.|
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]