EMBOSS: density

| density

## 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 -quad -qgraph cps
    Draw a nucleic acid density plot

    Created density.ps

Go to the output files for this example

Example 3

    % density tembl:x13776 -dual -dgraph cps
    Draw a nucleic acid density plot

    Created density.ps

Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers (* if not always prompted):
      [-seqall]            seqall     Nucleotide sequence(s) filename and optional
                                      format, or reference (input USA)
    *  -qgraph             xygraph    [$EMBOSS_GRAPHICS value, or x11] Quad
                                      (A+C+G+T) graph (ps, hpgl, hp7470, hp7580,
                                      meta, cps, x11, tekt, tek, none, data,
                                      xterm, png, gif)
    *  -dgraph             xygraph    [$EMBOSS_GRAPHICS value, or x11] Dual
                                      (AT+GC) graph (ps, hpgl, hp7470, hp7580,
                                      meta, cps, x11, tekt, tek, none, data,
                                      xterm, png, gif)
    *  -outfile            report     [*.density] Output report file name

       Additional (Optional) qualifiers:
       -window             integer    [100] Window length (Integer 1 or more)

       Advanced (Unprompted) qualifiers:
       -quad               toggle     [N] Produce graphic showing individual bases
       -dual               toggle     [N] Produce AT vs GC graphic

       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

       "-qgraph" 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

       "-dgraph" 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. 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-seqall] (Parameter 1) | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
-qgraph | Quad (A+C+G+T) graph | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
-dgraph | Dual (AT+GC) graph | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
-outfile | Output report file name | Report output file | <*>.density
Additional (Optional) qualifiers | Allowed values | Default
-window | Window length | Integer 1 or more | 100
Advanced (Unprompted) qualifiers | Allowed values | Default
-quad | Produce graphic showing individual bases | Toggle value Yes/No | No
-dual | Produce AT vs GC graphic | Toggle value Yes/No | No

## Input file format

density reads any normal sequence USAs.

### 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 of Pseudomonas
    RT   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 seqence 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   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
    XX

      [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: Tue 15 Jul 2008 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

    #---------------------------------------
    #---------------------------------------

    #---------------------------------------
    # Total_sequences: 1
    # Total_hitcount: 2068
    #---------------------------------------

### Output files for usage example 2

### Graphics File: density.ps

### Output files for usage example 3

### Graphics File: density.ps

## 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
sirna | Finds siRNA duplexes in mRNA
wordcount | Count and extract unique words in DNA sequence(s)

## Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
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