EMBOSS: density manual

density

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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:6.6.0.0

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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

Qualifier

Type

Description

Allowed values

Default

Standard (Mandatory) qualifiers

[-seqall]
(Parameter 1)

seqall

Nucleotide sequence(s) filename and optional format, or reference (input USA)

Readable sequence(s)

Required

-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

-outfile

report

Output report file name

(default -rformat table)

<*>.density

Additional (Optional) qualifiers

-window

integer

Window length

Integer 1 or more

100

-display

list

Select graph type

D	(Dual - graphic showing individual bases)
Q	(Quad - AT vs GC graphic)
none	(none)

none

Advanced (Unprompted) qualifiers

(none)

Associated qualifiers

"-seqall" associated seqall qualifiers

-sbegin1
-sbegin_seqall

integer

Start of each sequence to be used

Any integer value

-send1
-send_seqall

integer

End of each sequence to be used

Any integer value

-sreverse1
-sreverse_seqall

boolean

Reverse (if DNA)

Boolean value Yes/No

-sask1
-sask_seqall

boolean

Ask for begin/end/reverse

Boolean value Yes/No

-snucleotide1
-snucleotide_seqall

boolean

Sequence is nucleotide

Boolean value Yes/No

-sprotein1
-sprotein_seqall

boolean

Sequence is protein

Boolean value Yes/No

-slower1
-slower_seqall

boolean

Make lower case

Boolean value Yes/No

-supper1
-supper_seqall

boolean

Make upper case

Boolean value Yes/No

-scircular1
-scircular_seqall

boolean

Sequence is circular

Boolean value Yes/No

-squick1
-squick_seqall

boolean

Read id and sequence only

Boolean value Yes/No

-sformat1
-sformat_seqall

string

Input sequence format

Any string

-iquery1
-iquery_seqall

string

Input query fields or ID list

Any string

-ioffset1
-ioffset_seqall

integer

Input start position offset

Any integer value

-sdbname1
-sdbname_seqall

string

Database name

Any string

-sid1
-sid_seqall

string

Entryname

Any string

-ufo1
-ufo_seqall

string

UFO features

Any string

-fformat1
-fformat_seqall

string

Features format

Any string

-fopenfile1
-fopenfile_seqall

string

Features file name

Any string

"-graph" associated xygraph qualifiers

-gprompt

boolean

Graph prompting

Boolean value Yes/No

-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

"-outfile" associated report qualifiers

-rformat

string

Report format

Any string

table

-rname

string

Base file name

Any string

-rextension

string

File name extension

Any string

-rdirectory

string

Output directory

Any string

-raccshow

boolean

Show accession number in the report

Boolean value Yes/No

-rdesshow

boolean

Show description in the report

Boolean value Yes/No

-rscoreshow

boolean

Show the score in the report

Boolean value Yes/No

-rstrandshow

boolean

Show the nucleotide strand in the report

Boolean value Yes/No

-rusashow

boolean

Show the full USA in the report

Boolean value Yes/No

-rmaxall

integer

Maximum total hits to report

Any integer value

-rmaxseq

integer

Maximum hits to report for one sequence

Any integer value

General qualifiers

-auto

boolean

Turn off prompts

Boolean value Yes/No

-stdout

boolean

Write first file to standard output

Boolean value Yes/No

-filter

boolean

Read first file from standard input, write first file to standard output

Boolean value Yes/No

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

-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

-warning

boolean

Report warnings

Boolean value Yes/No

-error

boolean

Report errors

Boolean value Yes/No

-fatal

boolean

Report fatal errors

Boolean value Yes/No

-die

boolean

Report dying program messages

Boolean value Yes/No

-version

boolean

Report version number and exit

Boolean value Yes/No

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 INSDC.
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 INSDC.
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                   /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   misc_difference 1281
FT                   /replace="g"
FT                   /note="conflict"
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: Mon 15 Jul 2013 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.

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	Calculate nucleic acid melting temperature
freak	Generate residue/base frequency table or plot
isochore	Plot 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

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None

Wiki

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: tembl:x13776

Output file format

Output files for usage example

File: x13776.density

Output files for usage example 2

Graphics File: density.ps

Output files for usage example 3

Graphics File: density.ps

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments