August 9th 2018: We updated the server to version 1.4.0. (Changelog)
Find Seed PWMs
You can give your job a name to better distinguish between multiple runs.
A fasta file with at least 10 bound nucleotide sequences. Each sequence is assumed to carry at most one motif. If you have long sequences with several motifs, consider chopping them up into several shorter sequences.
A fasta file with sequences that represent the genomic background of the input sequences. If not provided, the background is estimated from the input sequences.
Length of patterns to be searched.
Patterns with a z-score threshold lower than this will not be considered.
Patterns with less than this amount of counts will not be considered.
The order for the background model. We recommend a background order of 2 for a realistic model of the genomic input. For very short motifs a background order of 1 or even 0 may be required to find the motif.
When checked, motifs can be both on the plus and minus strand.
The scoring function used for the optimization to IUPAC patterns.
When checked, the Expectation Maximization step will be skipped.