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|
isochore |
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Function
Plots isochores in DNA sequencesDescription
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 Plots 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
Plots isochores in DNA sequences
Version: EMBOSS:6.4.0.0
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
-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 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
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| [-outfile] (Parameter 2) |
outfile | Output file name | Output file | <*>.isochore |
| -graph | xygraph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg | EMBOSS_GRAPHICS value, or x11 |
| Additional (Optional) qualifiers | ||||
| -window | integer | Window size | Integer 1 or more | 1000 |
| -shift | integer | Shift increment | Integer 1 or more | 100 |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated sequence qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of the sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of the sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |
| -sid1 -sid_sequence |
string | Entryname | Any string | |
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |
| -fformat1 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
| "-graph" associated xygraph qualifiers | ||||
| -gprompt | boolean | Graph prompting | Boolean value Yes/No | N |
| -gdesc | string | Graph description | Any string | |
| -gtitle | string | Graph title | Any string | |
| -gsubtitle | string | Graph subtitle | Any string | |
| -gxtitle | string | Graph x axis title | Any string | |
| -gytitle | string | Graph y axis title | Any string | |
| -goutfile | string | Output file for non interactive displays | Any string | |
| -gdirectory | string | Output directory | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
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
![[isochore results]](isochore.1.isochore.gif)
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
- 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.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 | Calculates 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 RiceEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.