EMBOSS: chaos


Program chaos

Function

Create a chaos game representation plot for a sequence

Description

A box is drawn and an AGCT is drawn at each corner.

Starting from the middle, move half way to the corner of the box representing the first base in the sequence and draw a dot.

Then for each subsequent base move half way to the corresponding box corner and draw a dot.

Finally display the number and percentage values of AGCT bases.

Usage

Here is a sample session with chaos.

 chaos embl:eclac

click here for result

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequence]          sequence   Sequence USA
*  -graph              graph      Graph type
*  -outfile            outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -data               bool       Display as data


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
-outfile Output file name Output file <sequence>.chaos
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
-data Display as data Yes/No No

Input file format

Any DNA sequence USA.

Output file format

.ps file if postscipt output requested.

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

0 upon successful completion.

Known bugs

See also

Program nameDescription
chipsCodon usage statistics
codcmpCodon usage table comparison
compseqCounts the composition of dimer/trimer/etc words in a sequence
cpgplotPlot CpG rich areas
cpgreportReports all CpG rich regions
cuspCreate a codon usage table
diffseqFind differences (SNPs) between nearly identical sequences
dotmatcherDisplays a thresholded dotplot of two sequences
dotpathDisplays a non-overlapping wordmatch dotplot of two sequences
dottupDisplays a wordmatch dotplot of two sequences
einvertedFinds DNA inverted repeats
equicktandemFinds tandem repeats
etandemLooks for tandem repeats in a nucleotide sequence
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
palindromeLooks for inverted repeats in a nucleotide sequence
polydotDisplays all-against-all dotplots of a set of sequences
redataSearch REBASE for enzyme name, references, suppliers etc
restrictFinds restriction enzyme cleavage sites
showseqDisplay a sequence with features, translation etc
silentSilent mutation restriction enzyme scan
tfscanScans DNA sequences for transcription factors
wobbleWobble base plot
wordcountCounts words of a specified size in a DNA sequence

Author(s)

This application was written by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

History

 Completed 22nd March 1999.
 Last modified 14th June 1999.

Target users

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

Comments