EMBOSS: isochore manual

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   Sequence USA
  [-outfile]           outfile    Output file name
   -graph              xygraph    Graph type

   Additional (Optional) qualifiers:
   -window             integer    Window size
   -shift              integer    Shift increment

   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
   -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 deaths

Standard (Mandatory) qualifiers		Allowed values	Default
[-sequence] (Parameter 1)	Sequence USA	Readable sequence	Required
[-outfile] (Parameter 2)	Output file name	Output file	<sequence>.isochore
-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, xml	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   standard; DNA; HUM; 184666 BP.
XX
AC   AF129756;
XX
SV   AF129756.1
XX
DT   12-MAR-1999 (Rel. 59, Created)
DT   29-OCT-1999 (Rel. 61, Last updated, Version 2)
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; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
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   [2]
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   [3]
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
XX
DR   EPD; EP11158; HS_TNFA.
DR   EPD; EP11159; HS_TNFB.
DR   SPTREMBL; O00452; O00452.
DR   SPTREMBL; O14931; O14931.
DR   SPTREMBL; O95866; O95866.
DR   SPTREMBL; O95868; O95868.
DR   SPTREMBL; O95869; O95869.
DR   SPTREMBL; O95870; O95870.


  [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

None.

References

Bernardi G Isochores and the evolutionary genomics of vertebrates. Gene 2000 Jan 4;241(1):3-17
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
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.

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

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: tembl:AF129756

Output file format

Output files for usage example

File: af129756.iso

Graphics File: isochore.ps

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments