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dottup
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
Display a wordmatch dotplot of two sequences
Description
A dotplot is a graphical representation of the regions of similarity
between two sequences.
The two sequences are placed on the axes of a rectangular image and (in
the simplest forms of dotplot) wherever there is a similarity between
the sequences a dot is placed on the image.
Where the two sequences have substantial regions of similarity, many
dots align to form diagonal lines. It is therefore possible to see at a
glance where there are local regions of similarity as these will have
long diagonal lines. It is also easy to see other features such as
repeats (which form parallel diagonal lines), and insertions or
deletions (which form breaks or discontinuities in the diagonal lines).
dottup looks for places where words (tuples) of a specified length have
an exact match in both sequences and draws a diagonal line over the
position of these words. This is a fast, but not especially sensitive
way of creating dotplots. It is an acceptable method for displaying
regions of substantial similarity between two sequences.
Using a longer word (tuple) size displays less random noise, runs
extremely quickly, but is less sensitive. Shorter word sizes are more
sensitive to shorter or fragmentary regions of similarity, but also
display more random points of similarity (noise) and runs slower.
Usage
Here is a sample session with dottup
% dottup tembl:j01636 tembl:v00294 -wordsize=6 -gtitle="v00294 vs j01636" -graph
cps
Display a wordmatch dotplot of two sequences
Created dottup.ps
Go to the input files for this example
Go to the output files for this example
Command line arguments
Display a wordmatch dotplot of two sequences
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers (* if not always prompted):
[-asequence] sequence Sequence filename and optional format, or
reference (input USA)
[-bsequence] sequence Sequence filename and optional format, or
reference (input USA)
-wordsize integer [10] Word size (Integer 2 or more)
* -graph graph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tek, tekt, none, data, xterm, png, gif, pdf,
svg)
* -xygraph xygraph [$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 (* if not always prompted):
* -[no]boxit boolean [Y] Draw a box around dotplot
Advanced (Unprompted) qualifiers:
-stretch toggle [N] Use non-proportional axes
Associated qualifiers:
"-asequence" 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
-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
"-bsequence" associated qualifiers
-sbegin2 integer Start of the sequence to be used
-send2 integer End of the sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-scircular2 boolean Sequence is circular
-squick2 boolean Read id and sequence only
-sformat2 string Input sequence format
-iquery2 string Input query fields or ID list
-ioffset2 integer Input start position offset
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 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
"-xygraph" 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
dottup reads two nucleotide or protein 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:j01636' is a sequence entry in the example nucleic acid database
'tembl'
Database entry: tembl:j01636
ID J01636; SV 1; linear; genomic DNA; STD; PRO; 7477 BP.
XX
AC J01636; J01637; K01483; K01793;
XX
DT 30-NOV-1990 (Rel. 26, Created)
DT 09-SEP-2004 (Rel. 81, Last updated, Version 8)
XX
DE E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
XX
KW acetyltransferase; beta-D-galactosidase; galactosidase; lac operon;
KW lac repressor protein; lacA gene; lacI gene; lactose permease; lacY gene;
KW lacZ gene; mutagenesis; palindrome; promoter region;
KW thiogalactoside acetyltransferase.
XX
OS Escherichia coli
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC Enterobacteriaceae; Escherichia.
XX
RN [1]
RP 1243-1266
RX DOI; 10.1073/pnas.70.12.3581.
RX PUBMED; 4587255.
RA Gilbert W., Maxam A.;
RT "The nucleotide sequence of the lac operator";
RL Proc. Natl. Acad. Sci. U.S.A. 70(12):3581-3584(1973).
XX
RN [2]
RP 1246-1308
RX DOI; 10.1073/pnas.70.12.3585.
RX PUBMED; 4587256.
RA Maizels N.M.;
RT "The nucleotide sequence of the lactose messenger ribonucleic acid
RT transcribed from the UV5 promoter mutant of Escherichia coli";
RL Proc. Natl. Acad. Sci. U.S.A. 70(12):3585-3589(1973).
XX
RN [3]
RX PUBMED; 4598642.
RA Gilbert W., Maizels N., Maxam A.;
RT "Sequences of controlling regions of the lactose operon";
RL Cold Spring Harb. Symp. Quant. Biol. 38:845-855(1974).
XX
RN [4]
RA Gilbert W., Gralla J., Majors A.J., Maxam A.;
RT "Lactose operator sequences and the action of lac repressor";
RL (in) Sund H., Blauer G. (Eds.);
RL PROTEIN-LIGAND INTERACTIONS:193-207;
RL Walter de Gruyter, New York (1975)
XX
RN [5]
RP 1146-1282
[Part of this file has been deleted for brevity]
cgatttggct acatgacatc aaccatatca gcaaaagtga tacgggtatt atttttgccg 4560
ctatttctct gttctcgcta ttattccaac cgctgtttgg tctgctttct gacaaactcg 4620
ggctgcgcaa atacctgctg tggattatta ccggcatgtt agtgatgttt gcgccgttct 4680
ttatttttat cttcgggcca ctgttacaat acaacatttt agtaggatcg attgttggtg 4740
gtatttatct aggcttttgt tttaacgccg gtgcgccagc agtagaggca tttattgaga 4800
aagtcagccg tcgcagtaat ttcgaatttg gtcgcgcgcg gatgtttggc tgtgttggct 4860
gggcgctgtg tgcctcgatt gtcggcatca tgttcaccat caataatcag tttgttttct 4920
ggctgggctc tggctgtgca ctcatcctcg ccgttttact ctttttcgcc aaaacggatg 4980
cgccctcttc tgccacggtt gccaatgcgg taggtgccaa ccattcggca tttagcctta 5040
agctggcact ggaactgttc agacagccaa aactgtggtt tttgtcactg tatgttattg 5100
gcgtttcctg cacctacgat gtttttgacc aacagtttgc taatttcttt acttcgttct 5160
ttgctaccgg tgaacagggt acgcgggtat ttggctacgt aacgacaatg ggcgaattac 5220
ttaacgcctc gattatgttc tttgcgccac tgatcattaa tcgcatcggt gggaaaaacg 5280
ccctgctgct ggctggcact attatgtctg tacgtattat tggctcatcg ttcgccacct 5340
cagcgctgga agtggttatt ctgaaaacgc tgcatatgtt tgaagtaccg ttcctgctgg 5400
tgggctgctt taaatatatt accagccagt ttgaagtgcg tttttcagcg acgatttatc 5460
tggtctgttt ctgcttcttt aagcaactgg cgatgatttt tatgtctgta ctggcgggca 5520
atatgtatga aagcatcggt ttccagggcg cttatctggt gctgggtctg gtggcgctgg 5580
gcttcacctt aatttccgtg ttcacgctta gcggccccgg cccgctttcc ctgctgcgtc 5640
gtcaggtgaa tgaagtcgct taagcaatca atgtcggatg cggcgcgacg cttatccgac 5700
caacatatca taacggagtg atcgcattga acatgccaat gaccgaaaga ataagagcag 5760
gcaagctatt taccgatatg tgcgaaggct taccggaaaa aagacttcgt gggaaaacgt 5820
taatgtatga gtttaatcac tcgcatccat cagaagttga aaaaagagaa agcctgatta 5880
aagaaatgtt tgccacggta ggggaaaacg cctgggtaga accgcctgtc tatttctctt 5940
acggttccaa catccatata ggccgcaatt tttatgcaaa tttcaattta accattgtcg 6000
atgactacac ggtaacaatc ggtgataacg tactgattgc acccaacgtt actctttccg 6060
ttacgggaca ccctgtacac catgaattga gaaaaaacgg cgagatgtac tcttttccga 6120
taacgattgg caataacgtc tggatcggaa gtcatgtggt tattaatcca ggcgtcacca 6180
tcggggataa ttctgttatt ggcgcgggta gtatcgtcac aaaagacatt ccaccaaacg 6240
tcgtggcggc tggcgttcct tgtcgggtta ttcgcgaaat aaacgaccgg gataagcact 6300
attatttcaa agattataaa gttgaatcgt cagtttaaat tataaaaatt gcctgatacg 6360
ctgcgcttat caggcctaca agttcagcga tctacattag ccgcatccgg catgaacaaa 6420
gcgcaggaac aagcgtcgca tcatgcctct ttgacccaca gctgcggaaa acgtactggt 6480
gcaaaacgca gggttatgat catcagccca acgacgcaca gcgcatgaaa tgcccagtcc 6540
atcaggtaat tgccgctgat actacgcagc acgccagaaa accacggggc aagcccggcg 6600
atgataaaac cgattccctg cataaacgcc accagcttgc cagcaatagc cggttgcaca 6660
gagtgatcga gcgccagcag caaacagagc ggaaacgcgc cgcccagacc taacccacac 6720
accatcgccc acaataccgg caattgcatc ggcagccaga taaagccgca gaaccccacc 6780
agttgtaaca ccagcgccag cattaacagt ttgcgccgat cctgatggcg agccatagca 6840
ggcatcagca aagctcctgc ggcttgccca agcgtcatca atgccagtaa ggaaccgctg 6900
tactgcgcgc tggcaccaat ctcaatatag aaagcgggta accaggcaat caggctggcg 6960
taaccgccgt taatcagacc gaagtaaaca cccagcgtcc acgcgcgggg agtgaatacc 7020
acgcgaaccg gagtggttgt tgtcttgtgg gaagaggcga cctcgcgggc gctttgccac 7080
caccaggcaa agagcgcaac aacggcaggc agcgccacca ggcgagtgtt tgataccagg 7140
tttcgctatg ttgaactaac cagggcgtta tggcggcacc aagcccaccg ccgcccatca 7200
gagccgcgga ccacagcccc atcaccagtg gcgtgcgctg ctgaaaccgc cgtttaatca 7260
ccgaagcatc accgcctgaa tgatgccgat ccccacccca ccaagcagtg cgctgctaag 7320
cagcagcgca ctttgcgggt aaagctcacg catcaatgca ccgacggcaa tcagcaacag 7380
actgatggcg acactgcgac gttcgctgac atgctgatga agccagcttc cggccagcgc 7440
cagcccgccc atggtaacca ccggcagagc ggtcgac 7477
//
Database entry: tembl:v00294
ID V00294; SV 1; linear; genomic DNA; STD; PRO; 1113 BP.
XX
AC V00294;
XX
DT 09-JUN-1982 (Rel. 01, Created)
DT 10-FEB-1999 (Rel. 58, Last updated, Version 2)
XX
DE E. coli laci gene (codes for the lac repressor).
XX
KW DNA binding protein; repressor.
XX
OS Escherichia coli
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC Enterobacteriaceae; Escherichia.
XX
RN [1]
RP 1-1113
RX DOI; 10.1038/274765a0.
RX PUBMED; 355891.
RA Farabaugh P.J.;
RT "Sequence of the lacI gene";
RL Nature 274(5673):765-769(1978).
XX
CC KST ECO.LACI
XX
FH Key Location/Qualifiers
FH
FT source 1..1113
FT /organism="Escherichia coli"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:562"
FT CDS 31..1113
FT /transl_table=11
FT /note="reading frame"
FT /db_xref="GOA:P03023"
FT /db_xref="InterPro:IPR000843"
FT /db_xref="InterPro:IPR010982"
FT /db_xref="PDB:1CJG"
FT /db_xref="PDB:1EFA"
FT /db_xref="PDB:1JWL"
FT /db_xref="PDB:1JYE"
FT /db_xref="PDB:1JYF"
FT /db_xref="PDB:1L1M"
FT /db_xref="PDB:1LBG"
FT /db_xref="PDB:1LBH"
FT /db_xref="PDB:1LBI"
FT /db_xref="PDB:1LCC"
FT /db_xref="PDB:1LCD"
FT /db_xref="PDB:1LQC"
FT /db_xref="PDB:1LTP"
FT /db_xref="PDB:1OSL"
FT /db_xref="PDB:1TLF"
FT /db_xref="PDB:1Z04"
FT /db_xref="PDB:2BJC"
FT /db_xref="PDB:2KEI"
FT /db_xref="PDB:2KEJ"
FT /db_xref="PDB:2KEK"
FT /db_xref="PDB:2P9H"
FT /db_xref="PDB:2PAF"
FT /db_xref="PDB:2PE5"
FT /db_xref="PDB:3EDC"
FT /db_xref="UniProtKB/Swiss-Prot:P03023"
FT /protein_id="CAA23569.1"
FT /translation="MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAEL
FT NYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGV
FT EACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSH
FT EDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSA
FT MSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSC
FT YIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPR
FT ALADSLMQLARQVSRLESGQ"
XX
SQ Sequence 1113 BP; 249 A; 304 C; 322 G; 238 T; 0 other;
ccggaagaga gtcaattcag ggtggtgaat gtgaaaccag taacgttata cgatgtcgca 60
gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg tgaaccaggc cagccacgtt 120
tctgcgaaaa cgcgggaaaa agtggaagcg gcgatggcgg agctgaatta cattcccaac 180
cgcgtggcac aacaactggc gggcaaacag tcgttgctga ttggcgttgc cacctccagt 240
ctggccctgc acgcgccgtc gcaaattgtc gcggcgatta aatctcgcgc cgatcaactg 300
ggtgccagcg tggtggtgtc gatggtagaa cgaagcggcg tcgaagcctg taaagcggcg 360
gtgcacaatc ttctcgcgca acgcgtcagt gggctgatca ttaactatcc gctggatgac 420
caggatgcca ttgctgtgga agctgcctgc actaatgttc cggcgttatt tcttgatgtc 480
tctgaccaga cacccatcaa cagtattatt ttctcccatg aagacggtac gcgactgggc 540
gtggagcatc tggtcgcatt gggtcaccag caaatcgcgc tgttagcggg cccattaagt 600
tctgtctcgg cgcgtctgcg tctggctggc tggcataaat atctcactcg caatcaaatt 660
cagccgatag cggaacggga aggcgactgg agtgccatgt ccggttttca acaaaccatg 720
caaatgctga atgagggcat cgttcccact gcgatgctgg ttgccaacga tcagatggcg 780
ctgggcgcaa tgcgcgccat taccgagtcc gggctgcgcg ttggtgcgga tatctcggta 840
gtgggatacg acgataccga agacagctca tgttatatcc cgccgtcaac caccatcaaa 900
caggattttc gcctgctggg gcaaaccagc gtggaccgct tgctgcaact ctctcagggc 960
caggcggtga agggcaatca gctgttgccc gtctcactgg tgaaaagaaa aaccaccctg 1020
gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctggca 1080
cgacaggttt cccgactgga aagcgggcag tga 1113
//
Output file format
The output is to the specified graphics device.
The results can be output in one of several formats by using the
command-line qualifier -graph xxx, where 'xxx' is replaced by the name
of the required device. Support depends on the availability of
third-party software packages.
The device names that output to a file are: ps (postscript), cps
(colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.
The other available device names are: meta, x11 (xwindows), tek
(tek4107t), tekt (tektronix), xterm, text.
Output can be turned off by specifying none (null).
See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further
information on supported devices.
Output files for usage example
Graphics File: dottup.ps
[dottup results]
Data files
None.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
0 upon successful completion.
Known bugs
None.
See also
Program name Description
dotmatcher Draw a threshold dotplot of two sequences
dotpath Draw a non-overlapping wordmatch dotplot of two sequences
polydot Draw dotplots for all-against-all comparison of a sequence set
dotmatcher, by comparison, moves a window of specified length up each
diagonal and displays a line over the window if the sum of the
comparisons (using a substitution matrix) exceeds a threshold. It is
slower but much more sensitive.
Author(s)
Ian Longden formerly at:
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
CB10 1SA, UK.
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
History
Completed 24th March 1999.
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
|
