dreme [options] -p <primary sequence file> [-n <control sequence file>]
dreme-py3 [options] -p <primary sequence file> [-n <control sequence file>]
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.
A collection of sequences in FASTA format. The sequences should all be approximately the same length.
DREME outputs its results primarily as an HTML file named
dreme.html.
DREME also outputs a machine-readable XML file and a plain-text versions of its results,
named dreme.xml
and dreme.txt,
respectively.
Additionally DREME can output motif logos if the -png and/or -eps options are specified.
| Option | Parameter | Description | Default Behaviour | |
|---|---|---|---|---|
| Input/Output | ||||
| -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. | ||
| 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. | ||
| -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. | |
| Stopping Conditions | ||||
| -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. | |
| 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. | |||
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.
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