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

Input file format

Output file format

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Program nameDescription
chaosCreate a chaos game representation plot for a sequence
chipsCodon usage statistics
codcmpCodon usage table comparison
compseqCounts the composition of dimer/trimer/etc words in a sequence
cuspCreate a codon usage table
freakResidue/base frequency table or plot
geeceeCalculates the fractional GC content of nucleic acid sequences
isochorePlots isochores in large DNA sequences
newcpgreportReport CpG rich areas
newcpgseekReports CpG rich regions
tfscanScans DNA sequences for transcription factors
wordcountCounts 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.

Comments