
                               EMBOSS: wobble
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                                Program wobble
                                       
Function

   Wobble base plot
   
Description

   Wobble plots the third position variability as an indicator of a
   potential coding region.
   
   For each of the six possible translation frames, this plots a graph
   showing the percentage of 'G' and 'C' bases in the third position of
   codons in the frame within a window that is moved over the sequence.
   
   Bases other than 'G' and 'C' can be chosen with the -bases option.
   
   The Mean of the third base percentage value is drawn as a horizontal
   line across the plots.
   
Usage

   Here is a sample session with wobble. The example sequence is from
   Pseudomonas aeruginosa, which has a high G+C content and a very biased
   third codon position (if it can be G or C, it usually is).

% wobble
Wobble base plot
Input sequence: embl:paamir
Graph type [x11]:
Output file [paamir.wobble]:

   click here for the result
   
Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
   -graph              xygraph    Graph type
   -outf               outfile    Output file name

   Optional qualifiers:
   -window             integer    Window size in codons

   Advanced qualifiers:
   -bases              string     Bases used

   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
   [-sequence]
   (Parameter 1) Sequence USA Readable sequence Required
   -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
   -outf Output file name Output file <sequence>.wobble
   Optional qualifiers Allowed values Default
   -window Window size in codons Integer 1 or more 30
   Advanced qualifiers Allowed values Default
   -bases Bases used Any string is accepted GC
   
Input file format

   Normal nucleic acid sequence USA.
   
Output file format

   It plots a set of six graphs, one for each frame.
   
Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   "Sequence too short for window" - The sequence must be longer than 3
   times the window length.
   
   "Specifying ACG&T is meaningless" - When you use the option -bases to
   specify the bases to look for, it is pointless to specuy looking for
   all the possible bases as these should add to 100% all the time.
   
   "No bases specified" - Similarly you have to specify soem bases to
   look for otherwise you must plot a 0% line.
   
Exit status

   It always exist with a status of 0, unless a fatal error is given.
   
Known bugs

   None.
   
See also

   Program name                  Description
   getorf       Finds and extracts open reading frames (ORFs)
   marscan      Finds MAR/SAR sites in nucleic sequences
   plotorf      Plot potential open reading frames
   showorf      Pretty output of DNA translations
   
Author(s)

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

   Completed Spring 2000.
   
Target users

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