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Scanning for binding sites

STEME Options

Multiple motifs

Control how to find more than one motif.

--num-motifs (default=1): Number of motifs to look for.

--prediction-Z-threshold (default=0.3): The threshold on Z used to erase instances of motifs. The lower this is, the more instances will be erased.


Control the output location, format, writing logos, etc...

--output-dir (default=output): Output directory.

--meme-like-output (default=meme.txt): Produce MEME-like output so that it can be parsed by downstream tools.

--html-output (default=STEME.html): Produce HTML output.

--print-sites (default=False): Write a file containing the sites that were used to make the motif.

--dont-write-logos (default=False): Don’t write logos for motifs.

--write-em-logos (default=False): Write logos for motifs during EM algorithm.

--write-em-stats (default=False): Write statistics for EM algorithm.

--tomtom (default=[]): Run TOMTOM tool from the the MEME suite on the motifs using the specified motif databases.

--max-seqs-to-write (default=1000): Maximum number of sequences to write information about in output.

--max-sites-to-write (default=1000): Maximum number of sites to write information about in output.

--motif-name (default=STEME-): Name for output motifs.

Background model

Control the background model.

--bg-model-order (default=2): Order of the background Markov model.

--bg-fasta-file : If specified, STEME builds its background model from the sequences in this file rather than from the input sequences.

--back-dist-prior (default=1.0): Pseudo-counts for Markov background model.

Start finding

Control how starts are found.

--max-start-finding-time (default=0.0): How many seconds to dedicate to finding starts for each motif. If not given, STEME will look at each possible start (can be slow).

--min-num-sites : Minimum number of sites. Defaults to # sequences / 10.

--max-num-sites : Maximum number of sites. Defaults to 50% more than # sequences.

--width (default=[]): If specified, search for motifs of this width (can specify more than one).

--min-w (default=6): Minimum width of motif to find.

--max-w (default=14): Maximum width of motif to find.

--starts-per-motif (default=4): Number of starts to find per motif.

--use-seed : If specified, only use this seed as a start.

--starts-seed-pseudo-counts (default=0.5): Pseudo counts with which to smooth possible starting seeds.

--starts-speed-up (default=0): Speed up the start finding by ignoring so many potential starting points.

--candidate-starts-factor (default=1.41421356237): The factor for the geometric progression that determines which numbers of sites to try when start finding.


Control the behaviour of the Expectation Maximization algorithm.

--max-iters (default=1000): Maximum number of iterations for EM algorithm.

--dont-discretize (default=False): Don’t run discretisation after EM.

--convergence-distance (default=1e-05): Threshold between successive iterations at which to stop EM.

--wnsites (default=0.8): Weight on number of sites. Used when updating lambda in EM algorithm.

--em-seed-pseudo-counts (default=0.01): Pseudo counts for motif model in EM algorithm.

--epsilon (default=0.4): Allowed error in motif probabilities for EM algorithm.