Usage:

ama [options] <motif file> <sequence file> <background file>

Description:

The name AMA stands for "Average Motif Affinity". The program scores a set of DNA sequences given a DNA-binding motif, treating each position in the sequence as a possible binding event. The score is calculated by averaging the likelihood ratio scores for all feasible binding events to the given sequence and to its reverse strand. The binding strength at each potential site is defined as the likelihood ratio of the site under the motif versus under a zero-order background model provided by the user. By default, AMA reports the average motif affinity score and the p-value of that score for each sequence in its input. P-values are estimated analytically using the given zero-order background model.

AMA can instead be made to report the maximum of the likelihood ratio score, or the z-score of either the average or maximum likelihood score, using the options below.

If the input file contains more than one motif, the motifs will be processed consecutively.

Input:

Output:

AMA writes to standard out. The output format is either gff or CisML.

Options: