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.

Here is a sample session with freak:

% freak embl:hsfau Residue/base frequency table or plot Residue letters [gc]: Output file [hsfau.freak]:

Mandatory qualifiers (bold if not always prompted):

[-seqall] (seqall)

Sequence database USA.

-letters (string)

Residue letters.

-graph (xygraph)

Graph type.

-outfile (outfile)

Output filename.

Optional qualifiers:

-step (integer)

Stepping value.

-window (integer)

Averaging window.

Advanced qualifiers:

-plot (boolean)

Produce graphic.

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

Similar book on Amazon © 2008-2017.
If you may any questions please contact us: