freak reads one or more sequences and a set of bases or residues to search for. It then calculates the frequency of these bases/residues in a window as it moves along the sequence. The frequency is output to a data file or (optionally) plotted.
The frequency of bases/residues is calculated in a window that is moved along the sequence. The window size and stepping value (number of positions the window is moved along each time) may be specified.
|
|
The ouput consists of a title line and then two columns containing the position of the start of the window and then the frequency in that window of the bases or residues being searched for.
The default set of bases is cg which will calculate the frequency of G + C bases within the default moving window of 30 bases.