EMBOSS: wobble

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 nameDescription
getorfFinds and extracts open reading frames (ORFs)
marscanFinds MAR/SAR sites in nucleic sequences
plotorfPlot potential open reading frames
showorfPretty 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