freak
Function
Description
freak takes one or more sequences as input 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 default set of bases is 'cg' which will calculate the frequency of
'G' + 'C' bases within the default moving window of 30 bases.
Usage
Command line arguments
Input file format
freak reads normal sequence USAs.
Output file format
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.
Data files
None.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
Author(s)
History
Target users
Comments