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EMBOSS: chaos |
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.
The result is an image of a square sprinkled with dots. Areas which are devoid of dots (or heavily covered with dots) indicate short sequence motifs that are unusually infrequent (or frequent). The sequence of such motifs can be deduced by looking to see which quarter of teh square the region is in - the letter that this quarter belongs to is the first base of the motif. The quarter is then quartered again and the appropriate base letters are assigned to the corners of the quarter - the eigth part that the region is in gives the second base of the motif.
The process continues until you have identified the 1/16th or 1/32nd, etc. of the original square containing the unusual region and you now have the sequence of the motif.
% chaos embl:eclac Create a chaos game representation plot for a sequence Graph type [x11]:
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 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 |
-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 |
Program name | Description |
---|---|
banana | Bending and curvature plot in B-DNA |
btwisted | Calculates the twisting in a B-DNA sequence |
compseq | Counts the composition of dimer/trimer/etc words in a sequence |
dan | Calculates DNA RNA/DNA melting temperature |
freak | Residue/base frequency table or plot |
isochore | Plots isochores in large DNA sequences |
wordcount | Counts words of a specified size in a DNA sequence |
Completed 22nd March 1999. Last modified 14th June 1999.