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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:6.6.0.0
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
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.
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 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
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
|
