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<HTML>
<HEAD>
<TITLE>
EMBOSS: isochore
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
isochore
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Plots isochores in large DNA sequences
<H2>
Description
</H2>
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.
<p>
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.
<H2>
Usage
</H2>
<b>Here is a sample session with isochore</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>isochore tembl:AF129756 -graph cps </b>
Plots isochores in large DNA sequences
Output file [af129756.iso]: <b></b>
Created isochore.ps
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>Nucleotide sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output file name</td>
<td>Output file</td>
<td><i><*></i>.isochore</td>
</tr>
<tr>
<td>-graph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-window</td>
<td>Window size</td>
<td>Integer 1 or more</td>
<td>1000</td>
</tr>
<tr>
<td>-shift</td>
<td>Shift increment</td>
<td>Integer 1 or more</td>
<td>100</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>isochore</b> reads a normal nucleic acid USA.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:AF129756' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:AF129756</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
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
<font color=red> [Part of this file has been deleted for brevity]</font>
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
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: af129756.iso</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
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
<font color=red> [Part of this file has been deleted for brevity]</font>
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
</pre>
</td></tr></table><p>
<p><h3>Graphics File: isochore.ps</h3>
<p><img src="isochore.1.isochore.gif" alt="[isochore results]">
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
<ol>
<li>
Bernardi G
Isochores and the evolutionary genomics of vertebrates.
Gene 2000 Jan 4;241(1):3-17
<li>
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
<li>
Bernardi G
The human genome: organization and evolutionary history.
Annu Rev Genet 1995;29:445-76
</ol>
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with a status of 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="banana.html">banana</a></td>
<td>Bending and curvature plot in B-DNA</td>
</tr>
<tr>
<td><a href="btwisted.html">btwisted</a></td>
<td>Calculates the twisting in a B-DNA sequence</td>
</tr>
<tr>
<td><a href="chaos.html">chaos</a></td>
<td>Create a chaos game representation plot for a sequence</td>
</tr>
<tr>
<td><a href="compseq.html">compseq</a></td>
<td>Count composition of dimer/trimer/etc words in a sequence</td>
</tr>
<tr>
<td><a href="dan.html">dan</a></td>
<td>Calculates DNA RNA/DNA melting temperature</td>
</tr>
<tr>
<td><a href="freak.html">freak</a></td>
<td>Residue/base frequency table or plot</td>
</tr>
<tr>
<td><a href="sirna.html">sirna</a></td>
<td>Finds siRNA duplexes in mRNA</td>
</tr>
<tr>
<td><a href="wordcount.html">wordcount</a></td>
<td>Counts words of a specified size in a DNA sequence</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Peter Rice (pmr © ebi.ac.uk)
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
</BODY>
</HTML>
|
