Frequently asked questions: The PWMTools Web Site


General Questions

How can one cite this resource?

To properly cite the PWMTools project, please use the Website citation as follows:

  • - Ambrosini G., 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:

  • PWMij = log2(pij/bi) * c
where bi is the background frequency of base i, and pij is the site-specific 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.


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 log-odds 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 p-value for each motif identified by PWMScan?

The p-value for each motif identified by PWMScan is reported in the 8th filed of the output BED file containing the list of matches. The output BED file is in BED detailed format that is an extension of BED format used to enhance the track details page. In case of PWMScan, each match visualized at UCSC is thus linked to a description page that provides the name of the PWM, a link to our on-line PWMViwer tool (when applicable), and the p-value of the identified match.

Is the output of PWMScan oriented?

The PWMScan output file is oriented by default.

Last update July 2017