
                               EMBOSS: freak
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                                 Program freak
                                       
Function

   Residue/base frequency table or plot
   
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

   Here is a sample session with freak:

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

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-seqall]            seqall     Sequence database USA
   -letters            string     Residue letters
*  -graph              xygraph    Graph type
*  -outfile            outfile    Output file name

   Optional qualifiers:
   -step               integer    Stepping value
   -window             integer    Averaging window

   Advanced qualifiers:
   -plot               bool       Produce graphic

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-seqall]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -letters Residue letters Any string is accepted gc
   -graph Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png EMBOSS_GRAPHICS value, or x11
   -outfile Output file name Output file <sequence>.freak
   Optional qualifiers Allowed values Default
   -step Stepping value Any integer value 1
   -window Averaging window Any integer value 30
   Advanced qualifiers Allowed values Default
   -plot Produce graphic Yes/No No
   
Input file format

   Normal sequence USAs.
   
Output file format

   The output from the above example is:
     _________________________________________________________________
   
FREAK of HSFAU from 1 to 518 Window 30 Step 1

1          0.500000
2          0.533333
3          0.566667
4          0.533333
5          0.533333
6          0.566667
7          0.566667
8          0.566667
9          0.600000
10         0.633333
11         0.633333
12         0.666667
13         0.666667
14         0.666667
15         0.666667
16         0.633333
17         0.666667
18         0.633333
19         0.633333
20         0.633333
21         0.666667
22         0.666667
23         0.700000
24         0.733333
25         0.700000
26         0.666667
27         0.633333
28         0.600000
29         0.566667
30         0.600000
31         0.633333
32         0.600000
33         0.600000
34         0.633333
35         0.600000
36         0.600000

   [listing truncated for brevity]
   
   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.
   
See also

   Program name Description
   backtranseq Back translate a protein sequence
   banana Bending and curvature plot in B-DNA
   btwisted Calculates the twisting in a B-DNA sequence
   chaos Create a chaos game representation plot for a sequence
   charge Protein charge plot
   checktrans Reports STOP codons and ORF statistics of a protein
   sequence
   compseq Counts the composition of dimer/trimer/etc words in a sequence
   dan Calculates DNA RNA/DNA melting temperature
   emowse Protein identification by mass spectrometry
   iep Calculates the isoelectric point of a protein
   isochore Plots isochores in large DNA sequences
   mwfilter Filter noisy molwts from mass spec output
   octanol Displays protein hydropathy
   pepinfo Plots simple amino acid properties in parallel
   pepstats Protein statistics
   pepwindow Displays protein hydropathy
   pepwindowall Displays protein hydropathy of a set of sequences
   wordcount Counts words of a specified size in a DNA sequence
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

   Wriiten (Aug 2000) Alan Bleasby
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
