EMBOSS: wobble

Program wobble

Function

Wobble base plot

Description

Wobble plots the third position variability as an indicator of a potential coding region.

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

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 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

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	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

Output file format

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

Program name	Description
chaos	Create a chaos game representation plot for a sequence
chips	Codon usage statistics
codcmp	Codon usage table comparison
compseq	Counts the composition of dimer/trimer/etc words in a sequence
cusp	Create a codon usage table
freak	Residue/base frequency table or plot
geecee	Calculates the fractional GC content of nucleic acid sequences
isochore	Plots isochores in large DNA sequences
newcpgreport	Report CpG rich areas
newcpgseek	Reports CpG rich regions
tfscan	Scans DNA sequences for transcription factors
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

Target users

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