General Questions
How can one cite this resource?
To properly cite the PWMTools project, please use the Website citation as follows:
  Ambrosini G., PWMTools, http://ccg.vitalit.ch/pwmtools
In addition, you should cite the motif database that has been used for your analysis. You find the complete list of publications in the References Section on the Website.
What's the meaning of PWMs on this Server?
The formula we use to derive PWMs is the following, each element of the matrix, designated by PWMij (i=1,2,3,4, for A, C, G, T, and j is the site index) is given by:
where bi is the background frequency of base i, and pij is the sitespecific nucleotide frequency for nucleotide i at site j. c is a factor (constant) that we apply for convenience, by default c=100. If we assume a background frequency of 0.25 for each base, the sum (over i) of (pij/bi) is equal to 4.

PWMScan
What does the 5th field in the BED output field represent?
The 5th field of the output BED file represents the sequence score calculated using the position weight matrix (PWM).
When the PWM elements are represented by logodds values, the score of a sequence is calculated by adding the relevant values at each position of the PWM.
The sequence score gives an indication of how different the sequence is from a random one.
How can I get the pvalue for each motif identified by pwmscan?
The Pvalue can be obtained via the PWM viewer page (follow the link Score Distribution File). We may try to find a better way of offering this service.
Is the output of PWMScan oriented?
The PWMScan output file is oriented by default.
