EMBOSS: chaos

| chaos

## Function

Draw a chaos game representation plot for a nucleotide sequence

## Description

chaos creates a chaos game representation (CGR) plot for a nucleotide sequence. A CGR plot represents a nucleotide sequence as a square box with an `A`, `G`, `C`, or `T` nucleotide at each corner. The box contains dots, each one representing a dinucleotide. All overlapping dinucleotides from the start to the end of the sequence are plotted. Regions which are devoid of dots (or heavily covered with dots) indicate short sequence motifs that are unusually infrequent (or frequent). CGR plots depict base composition and sequentiality and is a unique visual representation of a sequence that complements more traditional linear representations.

## Algorithm

The plot is generated as follows. A box is drawn and an `A`, `G`, `C`, or `T` 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. The result is an image of a square sprinkled with dots.

## Usage

Here is a sample session with chaos

    % chaos tembl:j01636 -graph cps
    Draw a chaos game representation plot for a nucleotide sequence

    Created chaos.ps

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          sequence   Nucleotide sequence filename and optional
                                      format, or reference (input USA)
       -graph              graph      [$EMBOSS_GRAPHICS value, or x11] Graph type
                                      (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                      tekt, tek, none, data, xterm, png, gif)

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of the sequence to be used
       -send1              integer    End of the sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-graph" associated qualifiers
       -gprompt            boolean    Graph prompting
       -gdesc              string     Graph description
       -gtitle             string     Graph title
       -gsubtitle          string     Graph subtitle
       -gxtitle            string     Graph x axis title
       -gytitle            string     Graph y axis title
       -goutfile           string     Output file for non interactive displays
       -gdirectory         string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required
-graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

Any DNA sequence USA.

### Input files for usage example

'tembl:j01636' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:j01636

    ID   J01636; SV 1; linear; genomic DNA; STD; PRO; 7477 BP.
    XX
    AC   J01636; J01637; K01483; K01793;
    XX
    DT   30-NOV-1990 (Rel. 26, Created)
    DT   09-SEP-2004 (Rel. 81, Last updated, Version 8)
    XX
    DE   E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
    XX
    KW   acetyltransferase; beta-D-galactosidase; galactosidase; lac operon;
    KW   lac repressor protein; lacA gene; lacI gene; lactose permease; lacY gene;
    KW   lacZ gene; mutagenesis; palindrome; promoter region;
    KW   thiogalactoside acetyltransferase.
    XX
    OS   Escherichia coli
    OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
    OC   Enterobacteriaceae; Escherichia.
    XX
    RN   [1]
    RP   1243-1266
    RX   PUBMED; 4587255.
    RA   Gilbert W., Maxam A.;
    RT   "The nucleotide sequence of the lac operator";
    RL   Proc. Natl. Acad. Sci. U.S.A. 70(12):3581-3584(1973).
    XX
    RN   [2]
    RP   1246-1308
    RX   PUBMED; 4587256.
    RA   Maizels N.M.;
    RT   "The nucleotide sequence of the lactose messenger ribonucleic acid
    RT   transcribed from the UV5 promoter mutant of Escherichia coli";
    RL   Proc. Natl. Acad. Sci. U.S.A. 70(12):3585-3589(1973).
    XX
    RN   [3]
    RX   PUBMED; 4598642.
    RA   Gilbert W., Maizels N., Maxam A.;
    RT   "Sequences of controlling regions of the lactose operon";
    RL   Cold Spring Harb. Symp. Quant. Biol. 38:845-855(1974).
    XX
    RN   [4]
    RA   Gilbert W., Gralla J., Majors A.J., Maxam A.;
    RT   "Lactose operator sequences and the action of lac repressor";
    RL   (in) Sund H., Blauer G. (Eds.);
    RL   PROTEIN-LIGAND INTERACTIONS:193-207;
    RL   Walter de Gruyter, New York (1975)
    XX
    RN   [5]
    RP   1146-1282
    RX   PUBMED; 1088926.
    RA   Dickson R.C., Abelson J.N., Barnes W.M., Reznikoff W.S.;

      [Part of this file has been deleted for brevity]

         cgatttggct acatgacatc aaccatatca gcaaaagtga tacgggtatt atttttgccg      4560
         ctatttctct gttctcgcta ttattccaac cgctgtttgg tctgctttct gacaaactcg      4620
         ggctgcgcaa atacctgctg tggattatta ccggcatgtt agtgatgttt gcgccgttct      4680
         ttatttttat cttcgggcca ctgttacaat acaacatttt agtaggatcg attgttggtg      4740
         gtatttatct aggcttttgt tttaacgccg gtgcgccagc agtagaggca tttattgaga      4800
         aagtcagccg tcgcagtaat ttcgaatttg gtcgcgcgcg gatgtttggc tgtgttggct      4860
         gggcgctgtg tgcctcgatt gtcggcatca tgttcaccat caataatcag tttgttttct      4920
         ggctgggctc tggctgtgca ctcatcctcg ccgttttact ctttttcgcc aaaacggatg      4980
         cgccctcttc tgccacggtt gccaatgcgg taggtgccaa ccattcggca tttagcctta      5040
         agctggcact ggaactgttc agacagccaa aactgtggtt tttgtcactg tatgttattg      5100
         gcgtttcctg cacctacgat gtttttgacc aacagtttgc taatttcttt acttcgttct      5160
         ttgctaccgg tgaacagggt acgcgggtat ttggctacgt aacgacaatg ggcgaattac      5220
         ttaacgcctc gattatgttc tttgcgccac tgatcattaa tcgcatcggt gggaaaaacg      5280
         ccctgctgct ggctggcact attatgtctg tacgtattat tggctcatcg ttcgccacct      5340
         cagcgctgga agtggttatt ctgaaaacgc tgcatatgtt tgaagtaccg ttcctgctgg      5400
         tgggctgctt taaatatatt accagccagt ttgaagtgcg tttttcagcg acgatttatc      5460
         tggtctgttt ctgcttcttt aagcaactgg cgatgatttt tatgtctgta ctggcgggca      5520
         atatgtatga aagcatcggt ttccagggcg cttatctggt gctgggtctg gtggcgctgg      5580
         gcttcacctt aatttccgtg ttcacgctta gcggccccgg cccgctttcc ctgctgcgtc      5640
         gtcaggtgaa tgaagtcgct taagcaatca atgtcggatg cggcgcgacg cttatccgac      5700
         caacatatca taacggagtg atcgcattga acatgccaat gaccgaaaga ataagagcag      5760
         gcaagctatt taccgatatg tgcgaaggct taccggaaaa aagacttcgt gggaaaacgt      5820
         taatgtatga gtttaatcac tcgcatccat cagaagttga aaaaagagaa agcctgatta      5880
         aagaaatgtt tgccacggta ggggaaaacg cctgggtaga accgcctgtc tatttctctt      5940
         acggttccaa catccatata ggccgcaatt tttatgcaaa tttcaattta accattgtcg      6000
         atgactacac ggtaacaatc ggtgataacg tactgattgc acccaacgtt actctttccg      6060
         ttacgggaca ccctgtacac catgaattga gaaaaaacgg cgagatgtac tcttttccga      6120
         taacgattgg caataacgtc tggatcggaa gtcatgtggt tattaatcca ggcgtcacca      6180
         tcggggataa ttctgttatt ggcgcgggta gtatcgtcac aaaagacatt ccaccaaacg      6240
         tcgtggcggc tggcgttcct tgtcgggtta ttcgcgaaat aaacgaccgg gataagcact      6300
         attatttcaa agattataaa gttgaatcgt cagtttaaat tataaaaatt gcctgatacg      6360
         ctgcgcttat caggcctaca agttcagcga tctacattag ccgcatccgg catgaacaaa      6420
         gcgcaggaac aagcgtcgca tcatgcctct ttgacccaca gctgcggaaa acgtactggt      6480
         gcaaaacgca gggttatgat catcagccca acgacgcaca gcgcatgaaa tgcccagtcc      6540
         atcaggtaat tgccgctgat actacgcagc acgccagaaa accacggggc aagcccggcg      6600
         atgataaaac cgattccctg cataaacgcc accagcttgc cagcaatagc cggttgcaca      6660
         gagtgatcga gcgccagcag caaacagagc ggaaacgcgc cgcccagacc taacccacac      6720
         accatcgccc acaataccgg caattgcatc ggcagccaga taaagccgca gaaccccacc      6780
         agttgtaaca ccagcgccag cattaacagt ttgcgccgat cctgatggcg agccatagca      6840
         ggcatcagca aagctcctgc ggcttgccca agcgtcatca atgccagtaa ggaaccgctg      6900
         tactgcgcgc tggcaccaat ctcaatatag aaagcgggta accaggcaat caggctggcg      6960
         taaccgccgt taatcagacc gaagtaaaca cccagcgtcc acgcgcgggg agtgaatacc      7020
         acgcgaaccg gagtggttgt tgtcttgtgg gaagaggcga cctcgcgggc gctttgccac      7080
         caccaggcaa agagcgcaac aacggcaggc agcgccacca ggcgagtgtt tgataccagg      7140
         tttcgctatg ttgaactaac cagggcgtta tggcggcacc aagcccaccg ccgcccatca      7200
         gagccgcgga ccacagcccc atcaccagtg gcgtgcgctg ctgaaaccgc cgtttaatca      7260
         ccgaagcatc accgcctgaa tgatgccgat ccccacccca ccaagcagtg cgctgctaag      7320
         cagcagcgca ctttgcgggt aaagctcacg catcaatgca ccgacggcaa tcagcaacag      7380
         actgatggcg acactgcgac gttcgctgac atgctgatga agccagcttc cggccagcgc      7440
         cagcccgccc atggtaacca ccggcagagc ggtcgac                               7477
    //

## Output file format

### Output files for usage example

### Graphics File: chaos.ps

A graphics image is produced.

## Data files

None.

## Notes

Regions 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 the 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 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.

## References

1. Jeffrey (1990) Nucleic Acids Research 18: 2163-2170 "Chaos game representation of gene structure"

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

0 upon successful completion.

## Known bugs

None.

## See also

Program name | Description
--- | ---
banana | Plot bending and curvature data for B-DNA
btwisted | Calculate the twisting in a B-DNA sequence
compseq | Calculate the composition of unique words in sequences
dan | Calculates nucleic acid melting temperature
density | Draw a nucleic acid density plot
freak | Generate residue/base frequency table or plot
isochore | Plots isochores in DNA sequences
sirna | Finds siRNA duplexes in mRNA
wordcount | Count and extract unique words in DNA sequence(s)

## Author(s)

Ian Longden (il © sanger.ac.uk)
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

Completed 22nd March 1999.

## Target users

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

## Comments

None