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polydot
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 dotplots for all-against-all comparison of a sequence set
Description
polydot generates a dotplot for each of an all-against-all comparison
of a set of sequences. The dotplots are rendered on a single diagram.
The dotplot is an intuitive graphical representation of the regions of
similarity between two sequences. All positions from the first input
sequence are compared with all positions from the second input sequence
searching for exact matches between sequence regions ("words"). The two
sequences are the axes of the rectangular dotplot. Wherever there is
"similarity" between a word from each sequences a dot is plotted. The
wordsize is specified by the user. Optionally, information on the
sequence and location of all the exact matching regions may be written
to file as a feature file.
Algorithm
All sequence words of the specified size from the first input sequence
are compared with all words from the second input sequence and exact
matches identified. A line is plotted on the dotplot corresponding to
any exact matching words. Thus any local regions of identity correspond
to diagonals in the dotplot.
Usage
Here is a sample session with polydot
% polydot globins.fasta -gtitle="Polydot of globins.fasta" -graph cps
Draw dotplots for all-against-all comparison of a sequence set
Word size [6]:
Created polydot.ps
Go to the input files for this example
Go to the output files for this example
Command line arguments
Draw dotplots for all-against-all comparison of a sequence set
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers (* if not always prompted):
[-sequences] seqset File containing a sequence alignment
-wordsize integer [6] Word size (Integer 2 or more)
* -outfeat featout [unknown.gff] Output features UFO
-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)
Additional (Optional) qualifiers:
-[no]boxit boolean [Y] Draw a box around each dotplot
-dumpfeat toggle [N] Dump all matches as feature files
Advanced (Unprompted) qualifiers:
-gap integer [10] This specifies the size of the gap that
is used to separate the individual dotplots
in the display. The size is measured in
residues, as displayed in the output.
(Integer 0 or more)
Associated qualifiers:
"-sequences" 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
"-outfeat" associated qualifiers
-offormat string Output feature format
-ofopenfile string Features file name
-ofextension string File name extension
-ofdirectory string Output directory
-ofname string Base file name
-ofsingle boolean Separate file for each entry
"-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
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
polydot reads in a set of nucleic or protein sequences.
The sequences may or may not be aligned.
Input files for usage example
File: globins.fasta
>HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
EFTPPVQAAYQKVVAGVANALAHKYH
>HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
DFTPELQASYQKVVAGVANALAHKYH
>HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
VHASLDKFLASVSTVLTSKYR
>HBA_HORSE Sw:Hba_Horse => HBA_HORSE
VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
VHASLDKFLSSVSTVLTSKYR
>MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
AVIADTVAAGDAGFEKLMSMICILLRSAY
>LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA
Output file format
A graphical image is displayed on the specified graphics device.
Output files for usage example
Graphics File: polydot.ps
[polydot results]
Data files
None.
Notes
Where the two sequences have substantial regions of identity, longer
diagonal lines appear in the plot. It is possible to see at a glance
such local regions of identity. 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).
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
0 if successful.
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
dottup Display a wordmatch dotplot of two sequences
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 2nd June 1999.
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
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