                                  isochore



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Function

   Plot isochores in DNA sequences

Description

   isochore plots GC content in windows over a DNA sequence. The data may
   also be written to output file. The window wize and shift increment
   (the number of bases separating the start of each window) may be
   specified. isochore is suitable for use with 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
Plot isochores in 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

Plot isochores in DNA sequences
Version: EMBOSS:6.6.0.0

   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,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 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 and exit. 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
   -version            boolean    Report version number and exit


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 INSDC.
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 INSDC.
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

   [isochore results]

Data files

   None.

Notes

   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.

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       Plot bending and curvature data for B-DNA
                    btwisted     Calculate the twisting in a B-DNA sequence
                    chaos        Draw a chaos game representation plot for a nucleotide sequence
                    compseq      Calculate the composition of unique words in sequences
                    dan          Calculate nucleic acid melting temperature
                    density      Draw a nucleic acid density plot
                    freak        Generate residue/base frequency table or plot
                    wordcount    Count and extract unique words in molecular sequence(s)

Author(s)

   Peter            Rice
   European         Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton,         Cambridge CB10 1SD, UK

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

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

Comments

                    None
