isochore Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Plots 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 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 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] 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 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 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