density 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 Draw a nucleic acid density plot Description density produces a density plot of a nuleotide sequence. Usage Here is a sample session with density % density tembl:x13776 Draw a nucleic acid density plot Output report [x13776.density]: Go to the input files for this example Go to the output files for this example Example 2 % density tembl:x13776 -display quad -graph cps Draw a nucleic acid density plot Created density.ps Go to the output files for this example Example 3 % density tembl:x13776 -display dual -graph cps Draw a nucleic acid density plot Created density.ps Go to the output files for this example Command line arguments Draw a nucleic acid density plot Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers (* if not always prompted): [-seqall] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) * -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) * -outfile report [*.density] Output report file name (default -rformat table) Additional (Optional) qualifiers: -window integer [100] Window length (Integer 1 or more) -display menu [none] Select graph type (Values: D (Dual - graphic showing individual bases); Q (Quad - AT vs GC graphic); none (none)) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-seqall" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each 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 "-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 "-outfile" associated qualifiers -rformat string Report format -rname string Base file name -rextension string File name extension -rdirectory string Output directory -raccshow boolean Show accession number in the report -rdesshow boolean Show description in the report -rscoreshow boolean Show the score in the report -rstrandshow boolean Show the nucleotide strand in the report -rusashow boolean Show the full USA in the report -rmaxall integer Maximum total hits to report -rmaxseq integer Maximum hits to report for one sequence 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 density reads one or more nucleotide sequences. The input is a standard EMBOSS sequence query (also known as a 'USA'). Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application. The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. Input files for usage example 'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:x13776 ID X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP. XX AC X13776; M43175; XX DT 19-APR-1989 (Rel. 19, Created) DT 14-NOV-2006 (Rel. 89, Last updated, Version 24) XX DE Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation XX KW aliphatic amidase regulator; amiC gene; amiR gene. XX OS Pseudomonas aeruginosa OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; OC Pseudomonadaceae; Pseudomonas. XX RN [1] RP 1167-2167 RA Rice P.M.; RT ; RL Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases. RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG. XX RN [2] RP 1167-2167 RX DOI; 10.1016/0014-5793(89)80249-2. RX PUBMED; 2495988. RA Lowe N., Rice P.M., Drew R.E.; RT "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of RT Pseudomonas aeruginosa"; RL FEBS Lett. 246(1-2):39-43(1989). XX RN [3] RP 1-1292 RX PUBMED; 1907262. RA Wilson S., Drew R.; RT "Cloning and DNA sequence of amiC, a new gene regulating expression of the RT Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC RT product"; RL J. Bacteriol. 173(16):4914-4921(1991). XX RN [4] RP 1-2167 RA Rice P.M.; RT ; RL Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases. RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG. XX DR GOA; Q51417. DR InterPro; IPR003211; AmiSUreI_transpt. DR UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE. [Part of this file has been deleted for brevity] FT /replace="" FT /note="ClaI fragment deleted in pSW36, constitutive FT phenotype" FT misc_feature 1 FT /note="last base of an XhoI site" FT misc_feature 648..653 FT /note="end of 658bp XhoI fragment, deletion in pSW3 causes FT constitutive expression of amiE" FT conflict 1281 FT /replace="g" FT /citation=[3] XX SQ Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other; ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat 60 ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac 120 aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg 180 aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg 240 agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc 300 ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg 360 tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg 420 agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga 480 acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga 540 ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa 600 gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct 660 acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg 720 cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg 780 ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg 840 aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt 900 acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct 960 tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc 1020 tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt 1080 acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca 1140 gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc 1200 agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt 1260 ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg 1320 cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca 1380 gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt 1440 gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc 1500 gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc 1560 cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga 1620 tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa 1680 gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca 1740 ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct 1800 gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg 1860 aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt 1920 catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg 1980 gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct 2040 gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa 2100 ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt 2160 cctcgag 2167 // Output file format density outputs a graph to the specified graphics device. Output files for usage example File: x13776.density ######################################## # Program: density # Rundate: Fri 15 Jul 2011 12:00:00 # Commandline: density # [-seqall] tembl:x13776 # Report_format: table # Report_file: x13776.density ######################################## #======================================= # # Sequence: X13776 from: 1 to: 2167 # HitCount: 2068 # # Window size = 100 # #======================================= Start End Strand Score a c g t at gc 1 1 + 0.000 0.180 0.330 0.330 0.160 0.340 0.660 2 2 + 0.000 0.180 0.340 0.320 0.160 0.340 0.660 3 3 + 0.000 0.180 0.340 0.320 0.160 0.340 0.660 4 4 + 0.000 0.180 0.340 0.330 0.150 0.330 0.670 5 5 + 0.000 0.170 0.350 0.330 0.150 0.320 0.680 6 6 + 0.000 0.170 0.340 0.340 0.150 0.320 0.680 7 7 + 0.000 0.170 0.340 0.340 0.150 0.320 0.680 8 8 + 0.000 0.170 0.340 0.330 0.160 0.330 0.670 9 9 + 0.000 0.170 0.330 0.340 0.160 0.330 0.670 10 10 + 0.000 0.180 0.330 0.340 0.150 0.330 0.670 11 11 + 0.000 0.180 0.330 0.340 0.150 0.330 0.670 12 12 + 0.000 0.180 0.340 0.330 0.150 0.330 0.670 13 13 + 0.000 0.180 0.330 0.340 0.150 0.330 0.670 14 14 + 0.000 0.190 0.320 0.340 0.150 0.340 0.660 15 15 + 0.000 0.190 0.330 0.330 0.150 0.340 0.660 16 16 + 0.000 0.190 0.330 0.330 0.150 0.340 0.660 17 17 + 0.000 0.190 0.330 0.330 0.150 0.340 0.660 18 18 + 0.000 0.190 0.320 0.330 0.160 0.350 0.650 19 19 + 0.000 0.180 0.330 0.330 0.160 0.340 0.660 20 20 + 0.000 0.190 0.330 0.330 0.150 0.340 0.660 21 21 + 0.000 0.190 0.330 0.330 0.150 0.340 0.660 22 22 + 0.000 0.200 0.330 0.330 0.140 0.340 0.660 23 23 + 0.000 0.200 0.330 0.330 0.140 0.340 0.660 24 24 + 0.000 0.200 0.320 0.340 0.140 0.340 0.660 25 25 + 0.000 0.210 0.320 0.340 0.130 0.340 0.660 26 26 + 0.000 0.210 0.310 0.350 0.130 0.340 0.660 27 27 + 0.000 0.220 0.310 0.340 0.130 0.350 0.650 28 28 + 0.000 0.210 0.310 0.350 0.130 0.340 0.660 29 29 + 0.000 0.210 0.310 0.360 0.120 0.330 0.670 30 30 + 0.000 0.220 0.300 0.360 0.120 0.340 0.660 31 31 + 0.000 0.220 0.300 0.360 0.120 0.340 0.660 [Part of this file has been deleted for brevity] 2026 2026 + 0.000 0.110 0.340 0.330 0.220 0.330 0.670 2027 2027 + 0.000 0.110 0.330 0.340 0.220 0.330 0.670 2028 2028 + 0.000 0.110 0.330 0.340 0.220 0.330 0.670 2029 2029 + 0.000 0.110 0.330 0.340 0.220 0.330 0.670 2030 2030 + 0.000 0.110 0.330 0.330 0.230 0.340 0.660 2031 2031 + 0.000 0.110 0.330 0.320 0.240 0.350 0.650 2032 2032 + 0.000 0.110 0.330 0.320 0.240 0.350 0.650 2033 2033 + 0.000 0.120 0.320 0.320 0.240 0.360 0.640 2034 2034 + 0.000 0.120 0.330 0.310 0.240 0.360 0.640 2035 2035 + 0.000 0.120 0.340 0.300 0.240 0.360 0.640 2036 2036 + 0.000 0.120 0.330 0.300 0.250 0.370 0.630 2037 2037 + 0.000 0.130 0.330 0.290 0.250 0.380 0.620 2038 2038 + 0.000 0.130 0.330 0.290 0.250 0.380 0.620 2039 2039 + 0.000 0.130 0.340 0.280 0.250 0.380 0.620 2040 2040 + 0.000 0.130 0.330 0.280 0.260 0.390 0.610 2041 2041 + 0.000 0.130 0.330 0.290 0.250 0.380 0.620 2042 2042 + 0.000 0.130 0.330 0.280 0.260 0.390 0.610 2043 2043 + 0.000 0.120 0.330 0.290 0.260 0.380 0.620 2044 2044 + 0.000 0.120 0.330 0.290 0.260 0.380 0.620 2045 2045 + 0.000 0.120 0.320 0.300 0.260 0.380 0.620 2046 2046 + 0.000 0.120 0.320 0.290 0.270 0.390 0.610 2047 2047 + 0.000 0.120 0.310 0.300 0.270 0.390 0.610 2048 2048 + 0.000 0.120 0.300 0.310 0.270 0.390 0.610 2049 2049 + 0.000 0.120 0.310 0.310 0.260 0.380 0.620 2050 2050 + 0.000 0.120 0.320 0.300 0.260 0.380 0.620 2051 2051 + 0.000 0.120 0.310 0.310 0.260 0.380 0.620 2052 2052 + 0.000 0.120 0.320 0.300 0.260 0.380 0.620 2053 2053 + 0.000 0.120 0.330 0.300 0.250 0.370 0.630 2054 2054 + 0.000 0.130 0.320 0.300 0.250 0.380 0.620 2055 2055 + 0.000 0.140 0.320 0.290 0.250 0.390 0.610 2056 2056 + 0.000 0.140 0.320 0.290 0.250 0.390 0.610 2057 2057 + 0.000 0.140 0.330 0.280 0.250 0.390 0.610 2058 2058 + 0.000 0.150 0.330 0.280 0.240 0.390 0.610 2059 2059 + 0.000 0.150 0.330 0.290 0.230 0.380 0.620 2060 2060 + 0.000 0.150 0.320 0.290 0.240 0.390 0.610 2061 2061 + 0.000 0.150 0.320 0.290 0.240 0.390 0.610 2062 2062 + 0.000 0.140 0.330 0.290 0.240 0.380 0.620 2063 2063 + 0.000 0.140 0.330 0.290 0.240 0.380 0.620 2064 2064 + 0.000 0.140 0.320 0.290 0.250 0.390 0.610 2065 2065 + 0.000 0.140 0.330 0.290 0.240 0.380 0.620 2066 2066 + 0.000 0.140 0.330 0.290 0.240 0.380 0.620 2067 2067 + 0.000 0.140 0.330 0.290 0.240 0.380 0.620 2068 2068 + 0.000 0.140 0.330 0.300 0.230 0.370 0.630 #--------------------------------------- #--------------------------------------- #--------------------------------------- # Reported_sequences: 1 # Reported_hitcount: 2068 #--------------------------------------- Output files for usage example 2 Graphics File: density.ps [density results] Output files for usage example 3 Graphics File: density.ps [density results] Data files None Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 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 freak Generate residue/base frequency table or plot isochore Plots isochores in DNA sequences wordcount Count and extract unique words in molecular sequence(s) Author(s) Alan Bleasby 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