| isochore

## Function

Plots isochores in large DNA sequences

## Description

The nuclear genomes of vertebrates are mosaics of isochores, very long stretches (>300kb) of DNA that are homogeneous in base composition and are compositionally correlated with the coding sequences that they embed. Isochores can be partitioned in a small number of families that cover a range of GC levels (GC is the molar ratio of guanine+cytosine in DNA), which is narrow in cold-blooded vertebrates, but broad in warm-blooded vertebrates.

This application plots GC content over a sequence. It is intended for large sequences such as complete chromosomes or large genomic contigs, although interesting results can also be obtained from shorter sequences.

## Usage

Here is a sample session with isochore

    % isochore tembl:AF129756  -graph cps
    Plots isochores in large DNA sequences
    Output file [af129756.iso]:

    Created isochore.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)
      [-outfile]           outfile    [*.isochore] Output file name
       -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                      (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                      tekt, tek, none, data, xterm, png, gif)

       Additional (Optional) qualifiers:
       -window             integer    [1000] Window size (Integer 1 or more)
       -shift              integer    [100] Shift increment (Integer 1 or more)

       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

       "-outfile" associated qualifiers
       -odirectory2        string     Output directory

       "-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 standard output
       -filter             boolean    Read standard input, write 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
[-outfile] (Parameter 2) | Output file name | Output file | <*>.isochore
-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
-window | Window size | Integer 1 or more | 1000
-shift | Shift increment | Integer 1 or more | 100
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

isochore reads a normal nucleic acid USA.

### Input files for usage example

'tembl:AF129756' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:AF129756

    ID   AF129756; SV 1; linear; genomic DNA; STD; HUM; 184666 BP.
    XX
    AC   AF129756;
    XX
    DT   12-MAR-1999 (Rel. 59, Created)
    DT   14-NOV-2006 (Rel. 89, Last updated, Version 5)
    XX
    DE   Homo sapiens MSH55 gene, partial cds; and CLIC1, DDAH, G6b, G6c, G5b, G6d,
    DE   G6e, G6f, BAT5, G5b, CSK2B, BAT4, G4, Apo M, BAT3, BAT2, AIF-1, 1C7, LST-1,
    DE   LTB, TNF, and LTA genes, complete cds.
    XX
    KW   .
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
    OC   Homo.
    XX
    RN   [1]
    RP   1-184666
    RX   DOI; 10.1101/gr.1736803.
    RX   PUBMED; 14656967.
    RA   Xie T., Rowen L., Aguado B., Ahearn M.E., Madan A., Qin S., Campbell R.D.,
    RA   Hood L.;
    RT   "Analysis of the gene-dense major histocompatibility complex class III
    RT   region and its comparison to mouse";
    RL   Genome Res. 13(12):2621-2636(2003).
    XX
    RN   [2]
    RP   1-184666
    RA   Rowen L., Madan A., Qin S., Shaffer T., James R., Ratcliffe A., Abbasi N.,
    RA   Dickhoff R., Loretz C., Madan A., Dors M., Young J., Lasky S., Hood L.;
    RT   "Sequence of the human major histocompatibility complex class III region";
    RL   Unpublished.
    XX
    RN   [3]
    RP   1-184666
    RA   Rowen L.;
    RT   ;
    RL   Submitted (22-FEB-1999) to the EMBL/GenBank/DDBJ databases.
    RL   Department of Molecular Biotechnology, Box 357730 University of Washington,
    RL   Seattle, WA 98195, USA
    XX
    RN   [4]
    RP   1-184666
    RA   Rowen L.;
    RT   ;
    RL   Submitted (28-OCT-1999) to the EMBL/GenBank/DDBJ databases.
    RL   Multimegabase Sequencing Center, University of Washington, PO Box 357730,
    RL   Seattle, WA 98195, USA

      [Part of this file has been deleted for brevity]

         aaaccagttt accaccactc ctaacactaa acttaaatct gactctaaat gtaagtccaa    181740
         tctgagccac aagcctaaag ttgaacttta tcctgcttta tgaattattc atccattcct    181800
         ccatttagtg agtatctgcg tgcctaacac atgctgggca ttgtcctaag gcaggaggga    181860
         catggaggca aagggatcag agaaggtacc agcacctgtg gagcttgtat tccagtgagg    181920
         ccagacggaa aagaaagaaa ctgaagaaga aattggtact atgagaaaat aagacaggct    181980
         gatgttgtaa gagtggcagg gagctacttt taaatacagt agtcagcaaa atcctctttg    182040
         agtgtttggg tggcactgga gctgagaccc aaatgacaaa aaatagtgac caggtaaaag    182100
         tttgggagca aagcatttca ggtaaaggga gcagctactg caaaggctgg aaggcggaac    182160
         caagctgggg gtgttgacga caaacagaag gccagtgtgg ctggagcaga gagagagact    182220
         gggaggcggg tgggagatga ggtcagagag gagggcaggg gccaggtcat gcagggccat    182280
         gcaagaaggg taaagcctct agatttcatc cagccacagg aagcctttaa aggtcgtcag    182340
         agtgtgtggt gcgtgcgtgt gtgtgtgtgt gtgtgtgtgt gttgcagggg agagaggggg    182400
         agggagagag agagagagag agagaagagg gaggtgagca gaggtgattg gatttttttt    182460
         tcttttgaca tggtgtcttg ctctgtggcc taggctggag tgcagtggca ccatcatagc    182520
         ccactgcaac ctcaaaacca tgggctcaag tcatccttcc acctcagctt cccaagtatc    182580
         taggactaca ggtgtgtgcc actgtgcctg gctaatttta aaaaatattt taaaattttt    182640
         gttgagacag ggtctatgct gctcaggctg gtctcgaact cctggtttca agtgatctgc    182700
         ccatcttggc ctcccaaagt ttttttttgt tagtttgaga ggcggtttcg ctcgttgccc    182760
         aggctggagt gcaatgactg atctcatctc actgcaacct ctgcctcctg ggttcaagcg    182820
         attctcctgc ttcagcctcc caagtagctg ggattacagg tgcatgccac cattcccggc    182880
         taattttttg tatttagtag agatggggtt tcaccatgtt agtcaggctg atctcaaact    182940
         cctgacctca ggtgatccgc ctgcctcagc ctcccaaagt tttgggatta caggtgtgag    183000
         ccaccatgct gggccagcct cccaaagttt tgggattaca ggcatgagtc accacactgg    183060
         ccctggattt tttttctttc ttttttttgg agacggagtc tcactctgtt gcccaggctg    183120
         gagtgcaatg gcgtaatctc agctcactgc aacctctgct gcccgggttc aaacgattct    183180
         cctgtcttag cctcctgagt agctgggatt ataggtgcat gccaccatgc ctggctaatt    183240
         tttgtacttt tagtagagaa agtacaccat cttggccagg ctggtctcga actcctgacc    183300
         tcaggtgatc cacttgcgtc ggcctcccaa agtgctggga ttacaggcgt gagacaccgc    183360
         acccagcctt tttttttttt tttcttttaa gacagaatcg ctctgtcacc caggctggag    183420
         tgcagtggca caatctcggc tcactgcaac ctctgcctcc caggtttaag caatccacct    183480
         atgtcagtct cccaagtagc tgggattata ggtgcatgtc accatgcctg gctaattttt    183540
         gtacttttag tatagaaagt acaccatgtt ggccaggctg gtcttgaact cctgacctca    183600
         agtgatccgc ctgcctcagc ctcccgaagt gctggaatta cagacatgtg ccactgcacc    183660
         cggcctggtt ttttttttct aagagatgga gtctcacttt tctgcccagg ttggagtgca    183720
         atggcaccat catagctcac tgcagccttc aactcttggc ctcaggcaat ccttgcacct    183780
         tagcctcgca gtgttgggat tacaggcatg agccactgag ccttgcctgg actttttttt    183840
         ttttttgaga tggcgtctcg ctctgttgcc caggttggag tgctacggca tgatcttggc    183900
         tcactgcaac ttccacctcc caggttcaag cgattctctt gcctcggccc cccgagtagc    183960
         tgggattaca ggcatgcgcc accgtgcctg gctaattttg gtatttttag tagagatagg    184020
         gtttcatcat gttgggcagg ctggtcttga actcctgacc tcgtgatcca cccacctcgg    184080
         cctcccaaag tgctgggatt ataggcatag ccaacgcgcc cagcctggac ttgtttttaa    184140
         aagatcactg tggctcctgt gtttaggctg gctggtagga gacaggtggc agtggcattg    184200
         atggtgaaga gaaaatagtg gcagccatgg agatggagag aagtagacaa gtttgggata    184260
         tattatacat tccaggggta gaaacaacag gactagatga tggattgatg ggtgggagat    184320
         gtagatactg ggagagaagc aggattctga tggatggaaa aactaaaaaa ttctattttg    184380
         ggtgtggtaa gtctaagtct attagacatg caagtagaga tgtcactggg cagatacaca    184440
         tctggatttc aggggcaagg tccaagctag agaaagaaac ctgggcatgg tcagcatgag    184500
         gatggtgttt aaagccatgg aacttatctt gtgcatccct ataagacccc tttgaggcac    184560
         ttgtttcccc tcacaatgga tgcagtgcat cttccattct gaattccaga ggcaacaacc    184620
         tcctgctcct agaagctaaa ctctccagac ttagtcttct gaattc                   184666
    //

## Output file format

### Output files for usage example

### File: af129756.iso

    Position	Percent G+C 1 .. 184666
    500	0.471
    600	0.485
    700	0.482
    800	0.482
    900	0.475
    1000	0.489
    1100	0.496
    1200	0.499
    1300	0.479
    1400	0.477
    1500	0.466
    1600	0.442
    1700	0.451
    1800	0.455
    1900	0.470
    2000	0.455
    2100	0.443
    2200	0.440
    2300	0.458
    2400	0.467
    2500	0.480
    2600	0.493
    2700	0.501
    2800	0.498
    2900	0.501
    3000	0.508
    3100	0.522
    3200	0.514
    3300	0.518
    3400	0.515
    3500	0.517
    3600	0.530
    3700	0.517
    3800	0.527
    3900	0.509
    4000	0.500
    4100	0.490
    4200	0.496
    4300	0.492
    4400	0.479
    4500	0.470
    4600	0.464
    4700	0.463
    4800	0.460
    4900	0.467
    5000	0.476
    5100	0.477
    5200	0.479
    5300	0.476

      [Part of this file has been deleted for brevity]

    179100	0.406
    179200	0.422
    179300	0.412
    179400	0.402
    179500	0.397
    179600	0.397
    179700	0.398
    179800	0.402
    179900	0.436
    180000	0.456
    180100	0.472
    180200	0.456
    180300	0.458
    180400	0.462
    180500	0.487
    180600	0.477
    180700	0.471
    180800	0.479
    180900	0.477
    181000	0.463
    181100	0.454
    181200	0.448
    181300	0.436
    181400	0.444
    181500	0.425
    181600	0.435
    181700	0.446
    181800	0.459
    181900	0.460
    182000	0.471
    182100	0.485
    182200	0.483
    182300	0.498
    182400	0.495
    182500	0.505
    182600	0.513
    182700	0.514
    182800	0.500
    182900	0.493
    183000	0.500
    183100	0.491
    183200	0.502
    183300	0.508
    183400	0.509
    183500	0.515
    183600	0.517
    183700	0.515
    183800	0.508
    183900	0.500
    184000	0.492
    184100	0.493

### Graphics File: isochore.ps

## Data files

None.

## Notes

None.

## References

1. Bernardi G Isochores and the evolutionary genomics of vertebrates. Gene 2000 Jan 4;241(1):3-17
2. Pesole G, Bernardi G, Saccone C Isochore specificity of AUG initiator context of human genes. FEBS Lett 1999 Dec 24;464(1-2):60-2
3. Bernardi G The human genome: organization and evolutionary history. Annu Rev Genet 1995;29:445-76

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
banana | Bending and curvature plot in B-DNA
btwisted | Calculates the twisting in a B-DNA sequence
chaos | Create a chaos game representation plot for a sequence
compseq | Count composition of dimer/trimer/etc words in a sequence
dan | Calculates DNA RNA/DNA melting temperature
freak | Residue/base frequency table or plot
sirna | Finds siRNA duplexes in mRNA
wordcount | Counts words of a specified size in a DNA sequence

## Author(s)

Peter Rice (pmr © ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## History

## Target users

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

## Comments

None